EDIT: ok a lot of people are seeing this so i should probably clarify for those who haven't played persona 4

naoto isn't actually trans

her struggles are with misogyny in the workplace rather than with her gender identity

while she does seem to prefer dressing more masculine or androgynous and keeping her hair short, she is still a girl and identifies as such

in the game, she has to pretend to be a man due to women in male dominated fields not being taken seriously

her saying "Why couldn't I have been born male?" is just her saying she would be respected if she was a man

sorry if i explained this poorly i'm not good at this stuff

you are free to headcanon! just know that canonically, naoto is not trans