So technically Naoto would be Non-binary/Genderfluid Feminine.
I always hesitate to steadfastly gender a character when they don’t make it explicit themselves, but yes, Naoto definitely shows signs of being genderfluid. And so when people insist Naoto must be trans* I feel like people are ignoring the fact that genderfluid people exist just as much as the people who insist Naoto must be cis.
Canonically, Naoto presents as male and uses male pronouns in professional relationships or with strangers but is fine being called by feminine pronouns and explicitly identifies as female in close friendships and romantic relationships. And people are like, “Ugh, Atlus started writing a great trans* character and then copped out at the end and made them cis.” But noooooo, genderfluidity exists and is a thing and it really does fit Naoto’s gender experiences in Persona 4. Just like Kanji shows interest in Naoto presenting as male and female so I feel like it’s also disingenuous to assert he’s 100% straight or 100% gay.
I love Persona 4 because it has a very realistic portrayal of gender and sexuality that doesn’t try to fit things into any kind of definitive binary.
Buuut I’m writing an essay on this right now so I guess look for that soon.