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Fusion in Steven Universe, to the viewer, is a transparent way to represent non-heterosexual relationships in a show meant for children. It's not hard to see that when, despite Gems technically being non-gendered beings with hard-light projections for bodies, basically every Gem and fusion we see takes on a form meant to be read as feminine, from Pearl to the Diamonds, every Gem and fusion uses she/her pronouns, and the voice actors cast for Gem roles generally sound feminine. All of the visual and auditory cues to the viewer are intended to make us think of Gems as women, even though they're technically not. (That "technically" does some pretty heavy lifting out here in our world, given that for example, an Indiewire article about queer themes in Steven Universe titles itself 'Steven Universe’: 5 Ways This Kids Show Was Queer Before Its Lesbian Kiss.) The technicality of Gems not being women follows in grand sci-fi tradition of using non-human life-forms to reflect human society and its mores back at the humans watching it, but in such a way that the viewer has to think just enough about what they're seeing to connect it to their own world and experiences. Rebecca Sugar openly states that at least some of the gem relationships are based in their own relationships with family members and her husband, and that there was intense pushback from the network about including so much obvious and outright queerness in the show.
From the lens in-universe of Homeworld, however, they don't give a good goddamn about the supposed gender identities of the Gems engaging in fusion, because, again, genderless beings, but they really, really care about the relative castes and types of gems that are undergoing the fusion. The forbidden aspect of Ruby and Sapphire's relationship, the disdain of the "off-color" gems, and Pearl's reactions to Greg and Rose's relationship (outside of her own personal jealousy) all point to Homeworld's concern being about "mixing" of different Gems in cross-caste situations rather than any concern that entities of different presentations are combining.
Fusion, after all, is permitted by Homeworld in specific, tightly-controlled situations. The Giant Ruby that appears in "Hit the Diamond" (s03e05) as the fusion of five individual Rubies is clearly an acceptable fusion to defeat the threat of the Crystal Gems, and when the two Topaz appear as Aquamarine's hench-Gems and enforcers, they use their ability to fuse to capture their targets and hold them in place, as first demonstrated on-screen in "Are You My Dad?" (s04e24), and this is fine and expected. Rebecca Sugar explains on the Steven Universe podcast that Homeworld is the kind of place where everyone is expected to know what the function of a Gem is by looking at them, and that fusions across Gem types are difficult for Homeworld to square, because the Gems that went into that fusion become "off-color" from their original types, and also, that the new Gem in front of them is not something they can recognize, because it doesn't consist of the same components of the Gems that went into it. ("Homeworld Gems" - Vol.2/Ep.8)
Same gems fusing together, such that the resultant Gem is still easily identifiable and its purpose understood? Completely fine. Do it as needed to deal with the situation or the threat. Different Gems fusing together to create something that is not easily identifiable, whose purpose is not easily known from looking at them, and who may or may not have different thought and action processes? Completely unacceptable and outside the bounds of functioning society. The caste system of Homeworld is sufficiently brittle that the mere presence of an off-color or a cross-Gem fusion threatens to shatter it entirely, no doubt with many claims and worries of anarchy and lawlessness, so all the off-colors get shunned from society and have to live on the fringes or under the protection of a rebellious princess who has already committed sufficient number of taboos and forbidden things that Homeworld basically tried to blow up/corrupt her base planet and wash their hands of her. (Not that they knew it was the princess - they believed that a rebellious Gem had permanently killed their beloved Pink Diamond.)
There's still some aspects of queerness that show up in this construction and deconstruction of Homeworld's caste system. In the world of the viewer, many queer relationships don't make immediate and intuitive sense (a common question of a relationship between two men or two women is "so which one of you is the man?" or "which one of you is the woman?"), and there's certainly been enough moral panic expended about how having those "unnatural" relationships will completely destroy the fabric of society, a moral panic that hasn't really gone away as much as it has shifted targets over time, trying to find someone new to persecute when the old relationship or person has become sufficiently integrated and accepted by the society. At least for United States history, however, this construction of "knowing" who someone is, their background, their life, and their expected reactions, based on their outward appearance is rooted historically in racism and white supremacy. The current era adds transphobia to the racism and white supremacy and makes trans people the most prominent target, but the racism and white supremacy don't disappear.
Racism's history in the United States often revolves around the appearance of melanin in skin, any other coloration than paleness, or obvious "ethnic" features that indicate an ancestry that's somewhere outside of pale-skinned Europeans, so it's probably not by accident that the leader over a strict caste-basted society ends up being the White Diamond, and that she believes herself the gem that can speak to and for everyone. White diamonds are not colorless diamonds, but colorless diamonds often get referred to as white, in the same way that white people have a racial construction, but have done a significant amount of work to obscure that and think of them as the colorless (or "color-blind") people that everyone else is colored (inferiorly) in relation to. White supremacy then works to put white people at the top of that society, and relegates people of other colors to specific stereotypes and jobs, such that you can have a U.S. President talk about "Black jobs" as being endangered by immigrants of brown coloration as if this were some kind of immutable fact. Along with characterizations of people with melanin and people who immigrate from Latin American countries as having gang affiliations and being unable to rise above those situations without the noble assistance of white people plucking "the good ones" out and setting them on a better path. Usually as entertainers and sport players, performing for white audiences, and where the reactions and beliefs of those white audiences treated as the most important thing to the success or failure of the careers of those so "uplifted." Not usually in any way that can have impact on society or that gives them real power to change anything, and usually with the expectation that to succeed, they have to leave behind their context and adopt whiteness, or that they have to lean into the worst white stereotypes about their context.
And also, white people did an awful lot of making brown and black people their slaves and treating them as if they were not independent beings, and then punishing them so severely for stepping outside of their assigned role (often with death or severe injury) so as to discourage it from happening. Any parallels to draw between White Diamond's ability to override and enslave any other Gem to make them her mouthpiece and to behave in exactly the way she wants them to, and the society she built with constant threat of shattering Gems that step outside of their assigned roles, with a white Gem at the top and everyone else all subordinated, of course, are up to the reader to work out. As is the maternalistic attitude that White Diamond takes toward Steven when Steven continually says and does things that White Diamond doesn't want to acknowledge or that are outside her rigid conception of what Pink Diamond is supposed to do and be,. What's different is that when Steven retorts "I am a child; what's your excuse?" to her about his behavior compared to hers, White Diamond stops and thinks for a moment, instead of continuing on, dismissing it, or making excuses for it. (Which unravels everything, of course, as many things involving white supremacy spring apart when enough people in power stop to think about them and question whether they really are the best way of arranging life.)
(There's a tangent here, left to the reader to explore, about Bismuth and Pink Diamond/Rose Quartz, their different approaches to fighting Homeworld, and how it's not actually that hard for Bismuth to be read as the "angry Black woman" advocating for real, systemic change and Pink/Rose being the "polite white woman" with institutional \power who is actively hindering her, because she doesn't want the entire system to get knocked over, because doing so would deprive her of the power that she has been granted by the system. It's not related to fusion, the main topic of the essay, but it is another example of how White (Diamond) Supremacy is the structure that Homeworld relies upon for power and ruthlessly enforces on all those it believes it controls.)
The Gems that we meet also don't really have that much variation in their appearance, even if they are definitely varied in their personalities. The five Rubies in "Hit the Diamond" are nicknamed by Steven based on the placement of their gems in their bodies, but they're otherwise physically identical. Same with the Topaz Twins. In any situation where we see more than one of any particular Homeworld Gem, the designs for them are generally identical excepting for the placement of their Gem. There are animation reasons for this about reusing assets effectively, sure, but Gem society is also one built on being able to know what a Gem is and does simply by looking at them. Lots of humans believe this, too, and they are discomforted by people who do not follow the accepted cues, or whose cues read toward a gender identity that is not the one the person has. Transphobia works both by insisting people who don't conform to accepted presentations are dangerous and will put ideas in the heads of the impressionable as well as insinuating that there are people who are secretly part of the disfavored group that you can't spot by looking at them, and so you have to be vigilant to make sure that everyone around you behaves properly as well as looks properly.
For Gems, of course, whose bodies are, by their own admission, light projections, there's nothing stopping them from changing their appearance other than their own will and desire. Homeworld Gems are unlikely to do so. Peridot and Lapis don't change much except incorporating some stars into their expressions as part of their allegiance to the Crystal Gems. Much like humans, most Gems use and generally stay in their default forms, and appear to experience no discomfort or desire to change their shape into something else for long periods of time. If they had a gender, most Gems would be cisgender, much like most humans are.
Only two characters really incorporate shape-change into their regular selves over the course of Steven Universe. Pink Diamond who became Rose Quartz who gave birth to Steven goes through something that could be analogized to a binary transgender journey, since she starts as one type of Gem, with a specific appearance, and then, through effort and persistence, changes her default appearance to that of another Gem entirely (and fakes her death so that the previous life is left behind firmly), and then, later on in life, changes herself more to give birth to Steven, a hybrid of Gem and human who inherits his mother's Gem. Steven might be the only gendered Gem or part-Gem in the entirety of the Universe, and that makes him even stranger to the Gems he encounters, who have basically no frame of reference for him. Once the great reveal of "A Single Pale Rose" happens and we learn Steven's full lineage, most of the Homeworld Gems, including White Diamond, keep referring to him with the last referent they have, Pink Diamond, even though that was two whole identities ago. And their continued insistence that he is Pink Diamond, just shapeshifted into some other form, definitely reflects the deadnaming and attempts to push a trans individual back into the closet or to identifying as the person that others perceive them as, instead of who they are. it's not a coincidence that Pink Steven shouts "She's gone!" as rebuttal when White Diamond forcibly separates the Gem and the human sides of Steven in an attempt to make him into what she believes he is, rather than accepting him for what he is. The transphobia that Steven experiences is the one of people who refuse to believe that the person in front of them is real, even with all the correct cues and signs that would work for any other person to identify their gender. The Diamond Authority, their caste system, and White Diamond believe that there is an immutable facet of any given Gem that can't be changed, no matter what their appearance is. It's the argument that humans make when they're trying to hurt trans athletes or exclude them from spaces that are meant to be for one specific gender, almost always deployed against trans women as having "male energy" or that it would be "letting men play with women" and that would be unfair. Even against women who have had bottom surgery, hormone therapy, and any number of other procedures and interventions meant to give a woman the correct outside cues to society of their gender identity.
(Of course, most of the "this woman must secretly be a man" arguments get leveled at not-white women, either because they don't conform to white beauty and femininity standards, or because those white women are upset that they (or their daughters) are getting beaten by a not-white woman and they want to drop a mine in her pathway and subject her to humiliating examinations on the unfounded suspicion of being a man. "You can always tell," they'll claim, even though they're almost universally wrong.)
The other regular shape-changer is Amethyst, whose pathway isn't as much about complete change from one shape to another, but who engages in what would probably be seen as genderplay by being entirely okay with altering her appearance, either for functional appearances, for making a joke about something, or just because she wants to. A lot of the things we see Amethyst do throughout the series are things that other, more "proper" Gems like Pearl don't (or are actively repulsed by), but Amethyst shapeshifts a lot more than everyone else in the show. She also reworks herself much more, in terms of outfit colors and styles, over the course of Steven Universe. We find out fairly early on that Amethyst doesn't necessarily like the way she looks, or more correctly, she assumes that everyone else sees her as a defect, ugly, or otherwise someone who will never be able to join the ranks of the perfect Gems, regardless of whether she's in the Crystal Gems or Homeworld. It would be a reasonable assumption to believe that the reason Amethyst likes being in so many other different forms is because she doesn't like her default form, but again, Gems are basically formless and can take on whatever form they like. If Amethyst wanted to look like all the other Homeworld Amethysts, she could! (Well, once she knows what they look like. She was the last out of her Kindergarten, and everyone else had already left by the time she came into awareness.)
And, in fact, Amethyst does do just that! When she meets the Famethyst in "Gem Heist," Amethyst looks like a proper Homeworld Amethyst. Or at least, close enough to the rest of the Famethyst that Holly Blue Agate doesn't find her suspicious in any way. (Then again, Holly Blue doesn't like any of the Amethysts, so she's probably not inclined to examine a new one with any suspicious eye.) It's an effort for Amethyst to "pass" as a Homeworld Amethyst, because it's not her usual shape, but her facility and practice with shapeshifting lets her hold that shape for quite some time. Trans humans often are making decisions about how much "passing" they want to do for the group they are going to be a part of. Unsurprisingly, more effort goes into presentation when the consequences for not meeting the expectation of looking and acting the part are going to be more severe. (Everybody in "Gem Heist" is doing some amount of trying to "pass," but for most of them, it's about remembering what actions the role requires, rather than having to change their appearances as well.)
Thankfully, Amethyst doesn't have to hold the stranger shape forever, because her fam accepts her in her usual shape. It probably helps that the Famethyst already has a couple of other Gems that are "defective" in the skinny Jasper and the short Carnelian, so Crystal Gem Amethyst doesn't have to try and "pass" all the time around them, and they accept her for herself as part of their family immediately. It's really good for Amethyst that her "birth" family (the Famethyst) and her "chosen" family (the Crystal Gems) both accept her for who she is, giving her a solid group of Gems who support her unconditionally, even if some of the Crystal Gems don't always get along with her. Amethyst's biggest issue with herself is her self-image, and what she assumes other people must be thinking about her ability and competence in relationship to her appearance.
Amethyst's deep-seated self-esteem issues mirror a specific kind of transphobia, the comments that declare that the trans person will never "pass" or will never be a true member of the gender they wish to present. Once again, "You can always tell" rears its ugly head, or there's a narrative that unless you can and look, act, and sound the part of what you want to present flawlessly, there's no business in trying, because you will never be accepted unless you conform to all of the stereotypes and hyper-perform your chosen presentation. Even in the Gem society, though, there's still enough variations among the Amethysts in the Famethyst, with coloration choices and gem placements, that there's no such thing as the Platonic ideal of the Gem that everyone is compared against. Same thing with the Rubies from "Hit the Diamond" - if they were all exactly alike, Steven wouldn't be able to nickname all of them based on their Gem placement. There's definitely an image that each Gem is supposed to conform to and make it easy for them to be identified, but both Gems and human women have enough variation in their presentation, while still falling under the category of Gem (or woman) that trying to exclude someone from the category based on their presentation inevitably excludes someone who most of the beings around them would agree is part of the category.
But when the conception of sex and gender that is the foundation for most arguments against trans people ever being able to pass, or that trans people can't ever be the gender they've transitioned to, is rooted in colonialist, white supremacist ideas of what is acceptable and desirable and what is not, and is then further buttressed by a belief that certain presentations have specific, inescapable roles to play, we find that the Gems who disapprove of cross-Gem fusion often do so because they refuse to read the resulting Gem properly, Gems that refuse to believe that a Gem who changed form has changed themselves, because they refuse to read the result properly, and Gems who look down on those who look differently, because they refuse to believe properly, are all buying into and perpetuating White (Diamond) Supremacy.
And nowhere do we have to look for the implementation of that, and the understanding that the State monopoly on violence allows them to implement what they believe is proper behavior, than the Diamond Authority itself. Yellow Diamond exacts physical violence upon Gems, "poofing" them with her disruptors. Blue Diamond exacts emotional violence on them, with her ability to project an emotional state on everyone around her. While Pink Diamond's role is not well-defined, her Diamond ability to "bubble" and imprison other Gems in artifacts or in their Gem state indefinitely suggests Pink's role in the system is creative and intellectual violence, and her job would be to create stasis and prevent "dangerous" ideas from being allowed to take root in Homeworld society, by bubbling away those who have them indefinitely. Most likely, then, a Pink that didn't choose to rebel when seeing evidence that lesser beings were capable of the same creativity as Gems would likely be on crusade against any and all "off-colors" that she came across, using her authority and power to ensure that nothing ever arose to challenge the Diamond Authority and that nobody ever fused in a way that wasn't permitted by Homeworld.
Thus, we end where we've begun, with fusion, shape-change, and other actions that step outside the assigned roles that Gems receive at birth all working as resistance against the system imposed upon all Homeworld Gems from White Diamond. Fusion runs on compatible emotional states, and the most stable fusions that we see in Steven Universe run on joy and happiness and having positive connections between those getting fused. It's always possible for someone to fuse grudgingly or even with hostility and subjugation in mind, but those fusions require more effort to maintain. Thus, Steven Universe gives us one last piece of information: queer joy is one of the most effective ways of resisting a system that threatens you with violence just for existing. It's never explicitly stated as such in the show itself, but it's clear that love and joy are the things that carry the day all throughout every season of Steven Universe, and that even at the end, the power of love and joy is how Steven is able to defeat White Diamond and get her to change her ways.
So, to borrow a bit from Fryman, remember to always Keep Beach City Queer.