Yeah, so the trope really isn't shocking coming from Atlus' who has a penchant for homophobia.
I haven't beaten P5 because it's a bad game, so I have no idea what trans related stuff is in that, but people need to realize that more than anything this is a cultural issue and Japan is way, way behind the times on LGBT related stuff. It can be a very conservative society in relation to gender and sexuality. That said, I do think trans people have more acceptance there than gay people. Kinda like in other Asian countries. So Atlus pulling this isn't really a surprise and kinda the norm, unfortunately.
And yeah, I doubt they talked to once single trans person.