consider this take: Naoto is MTF, not FTM
it’s certainly pretty easy to read characters who are Officially Women, but who present traditionally masculine to help them succeed in a male-dominated misogynistic society, as trans women? since that’s something we kinda do automatically thanks to cisnormativity. naoto, mulan, pidge voltron, and sheik ocarina of time can all be read in this way, at least at a basic level.
however, depending on the specifics of the work in question, reading the character as transfem might have problematic implications. i’m not nearly as much an expert on naoto persona 4 as i am on chihiro danganronpa, but i’m given to understand reading naoto as transfem does have similar issues? i’d go into detail if i actually knew more about the game. i think kanji is gay and into naoto? maybe?
also tbh reading sheik as a woman is kinda weird given they only actually needed to Not Look Like Zelda? presenting traditionally masculine was entirely their choice. so sheik’s probably a dude too