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Chogent makes sense because of their similarities and differences. They're like two sides of the same coin; they're each other's enemies but they experience very similar things in terms of relationship with others.
Both are attached to one person, becoming someone only to support them and be there for them while neglecting their own needs.
Victim and Agent's relationship:
Their relationship, I would call one sided. From the way we see Agent treat Victim, we can see that he is very loyal and respectful towards him, working to help him reach his goals without often questioning him. But not only that, we see that he is potentially just attached to him as a person and not just as an employee.
For example in AVA 13, where he would catch Victim from falling, where he would try to step in Victim and Dark's fight, and in Skim's storyboard (yea i know it's not canon but I wanna include it…) where when Victim got slashed, Agent ran to him urging to help.
But we don't see Victim return this care, is the problem.
Victim almost uses Agent for his own advantage. He doesn't even let Agent touch him. Agent tried to once which we don't even see a lot because during AVA 11, Agent tried one but as soon as is touch was denied, he never tried to touch him again because he understands those are Victim's boundaries. (Even though, we still see him almost touching him, his arms hovering around him and stuff.)
I believe Victim even cooperates with Dark more than he does with Agent. Because as we know, Victim wants Mitsi back, and Dark made it seem as if he had a shortcut to that. He accepts touch from Dark, he listens to Dark, because Agent doesn't have an immediate solution to what he wants. He most likely didn't even tell Agent about Dark, as he shrugs when questioned "what was up" with him by one of the workers. And even then, Agent still trusted whatever Victim was planning.
In Victim's death, he doesn't acknowledge Agent as he runs to him, instead putting his attention towards Mitsi. In Agent's death, Victim is the brightest thing reflecting his shades.
Dark And Chosen's Relationship:
Much like Agent, Chosen is devoted to Dark and it is canon that they "used to" be close.
Now, Chosen isn't innocent. He was the one who dragged Dark into causing destruction, he's of course killed a lot of people in this universe but we do see that he's clearly guilty of those actions as of the most recent episodes and that's when the toxic part of their friendship comes to play.
Chosen is often shown to struggle with boundaries. He either breaks them or fails to set them with Dark.
An example of this is in Ep 0, where Chosen tries stop Dark from bombing his creation, he gives in when Dark gets upset at being denied. Another example of this is in the Newgrounds War, Chosen tries to stop Dark from killing Mitsi and says nothing when he fails, instead giving him a high five afterwards. He clearly cares about Dark a lot and doesn't want to make him upset.
And we have been shown many times that Dark cares about only one thing; Having fun. He has fun causing destruction, he has fun killing people. And if his closest friend doesn't want that, he replaces him with somebody else who he believes could understand him better. Much like Victim, Dark only likes Chosen when he gives him something he wants.
In conclusion of Chosen and Agent's similarities, they both have a one sided relationship with the one person they're devoted to. So, would that make them a good pair for each other?
Relationship possibilities:
Them as a pair I believe would be healthier as they can both benefit from being with each other.
Chosen, who has his whole life lived with violence, could be taught gentleness and of course, boundaries, as Agent is a person who seems to respect them a lot.
And Agent, who is used to giving and never receiving, could be given the same support and care, as Chosen is shown to be shown to support those who he values.
Together, they can grow as better people by simply being there for each other.