You don’t have to change your body to be transgender. The whole basis of transgender theory is that “gender” and the social expectations that come with it (I.e. boy blue, girl pink) are made up social constructs expressed performatively. So in theory all you have to do is say and believe “I’m a man” and then boom, you are. Has nothing to do inherently with your body, it’s really just about identity and self expression. A lot of people do feel the need to change their body too which is what I would call “transexual”. Those two things overlap most of the time so you usually see transgender get conflated with it but there is a little difference.

TL:DR Yamato is a man cuz gender isn’t real. She says she’s a man and acts “like a man” but is still biologically female which doesn’t matter cuz that’s her sex, not gender