1. The reaction drawing ire, VIncent's horrified expression, is a running gag in the game: it's his reaction to any vaguely sexual situation he encounters, because he's already engaged to another woman in-story and is terrified to unconsciously cheat on her. Later in the plot, he starts making it to any situation that changes the status quo of his life in any major way, since -- you know -- his life and relationships are collapsing.
2. The entire driving point of Catherine is that Vincent and his friends are abject scumbags; they drink all day, everyone other than Vincent is prone to openly objectifying women, and most of them don't have any real aspirations. This is what gets them sentenced to the allegorical nightmare world where they have to deal with their romantic failings, and it's what pushes Vincent to mature as a character and stop treating both of his potential partners like garbage.
3. Erica, the existing trans character in the original game, isn't a negative depiction at all. The game has her as the only rational moral center Vincent ever gets among all of the friends telling him to lie and cheat, and with regards to certain actions undertaken by both love interests, she's pretty much the only genuinely decent person in the whole story. The deadnaming gag by which she's revealed to be trans is unfortunate, but note that this scene only takes place in the best "light side" ending, and the only one freaked out by the reveal is the youngest man who's undergone the least character growth -- Vincent and the other friends explicitly already knew.
4. Atlus may have a (well-deserved) reputation for generally failing at LGBT+ representation, but everyone conveniently leaves out that Persona 5 featured a supporting trans character in Lala Escargot, who is depicted positively and respectfully, always referred to with female pronouns, and is -- like Erica -- a responsible moral figure despite having a much smaller role in the game; enough that of all people, she placed first in Japan's NPC popularity poll. This trans-positive track record is exceptionally rare for big studios of any kind, let alone Japanese game developers (the only other Japanese dev who comes to mind as successful in this regard is Yoko Taro).
5. The simplest fact of the matter of all is that by nature of being a romance option in this game, Rin will have Vincent able to pursue and grow more comfortable with her, and will have at least a few possible endings where the two of them are together. That's just how the game works. Even if his shitty reaction is indicative of his trans panic, her path must include him growing as a person in some way like the other two do, and they'll either end up splitting peacefully or pursuing the relationship further if the path hews to similar beats as the other two. But people have lost the ability to judge things after all information is available, so I doubt even confirmation that Rin is trans and a positive in-game path will quell the outrage.