Souji’s only ever been jealous of Rise...and Shadows with Confusion. He’d never been jealous before he’d developed his little crush on Yosuke. But then, before Inaba, in general he hadn’t had anything to lose.
He knows that it’s a silly emotion. Is angry that it’s not rational, that another person (much less a Shadow) isn’t going to be what drives Yosuke away. In the end, if anything it’ll be Yosuke who drives Yosuke away. Other than showing him that he’s not going to immediately get treated like a leper the second anyone so much as suspects he likes a guy (Souji, no less, and if certain sources were telling the truth it’s actually pretty common and no one would be especially surprised if they found others in the same situation) and that it’s not a problem to really express what he feels, there’s not really much Souji can do.
Yosuke wouldn’t shut up about Rise, at the beginning, and even when he’d stopped being obvious about it, he’d still been paying a little too much attention to her. He’d stopped, but it’d probably taken an intervention via Yukiko or Chie to actually get him to realize how much it’d hurt.
Yosuke had taken a stand and talked to Rise, letting her know that she was out of line. So Souji’s no longer as worried about that front. That took a lot of courage to do, and for a guy like Yosuke it’s no empty gesture.
The Amorous Snake was worse. Watching Yosuke’s eyes glaze over and take on a serious, loving look. Charge Souji with a controlled rage that he couldn’t remember having seen other than from Yosuke’s Shadow. It’s, oddly enough, not the worst thing to have the one he loves trying to kill him. It’s worse knowing that a spell could be enough to take Yosuke away, and even though status effects have always worn off before, it doesn’t mean that they might not next time. He makes sure he always has a Persona with Patra or an Amrita Soda and Yukiko with him, just to be careful.
They don’t actually know it, but they actually take it better than the Persona team from Gekkoukan. The terminology used is different. Labeling the status effect as Charm or Confusion given its result makes a fair amount of sense, and it’s not like they’d ever met to compare notes. The SEES team used mainly terminology that had been developed by Kirijo researchers, while the Inaba Investigation Team came up with names of Shadows while sitting in the food court, eating and occasionally teasing as they discussed the case. Some things are the same for all wielding Personas and fighting Shadows. Some things aren’t.
Maybe it’s the fact that, for the most part, they have more of a sense of team cohesion. The SEES team is a little less of a team and more of a collection of people fighting for the same cause. It doesn’t help that they don’t all trust each other, or that they have different agendas, or that they don’t really hang out as a team outside of battle. (They actually develop the greatest closeness as a team after they lose some of their members.) The Inaba Investigation Team may seem like it’s not a united force when they tease, but they trust each other in battle. They’ll without hesitation throw themselves in harm’s way for another team member (mostly Souji, but the others too) and exhaust themselves casting spells to defeat the threatening Shadows or heal the others. More than that, they’ll help the others out if they have a problem, even if they might tease them first, and they’ll probably go far out of their way to help out, even if it inconveniences them.
Both that and the previous fact, that the Charm doesn’t bother the Inaba IT as much, are probably due to one simple difference: the SEES team definitely faced their fears and grew as people, there’s no doubt about that, but the Persona-Users from Inaba had to face their Shadows. And they weren’t alone when doing so. A part of their mind had attacked their friends. Conversely, being attacked by their friends or by a part of their friends wasn’t anything new. There’s no blame or fear, just the need to fight until the other comes to their senses and the battle is over.
The Inaba IT is often oblivious. Souji is lucky, though. Since whatever happened with Yosuke, the Prince of Junes has been paying more attention to the team’s Leader, and the affection he’s been showing, all the more precious for the fact that Yosuke doesn’t find it easy, has done well at making the jealousy vanish like it’s just a Shadow’s ailment.