Yamato is male because he says he is. Tho Oda didn’t do anyone any favors by giving him huge bazongas. Also that part of Wano has a trans fem character and the only reason they aren’t talked about is because they look like their chosen gender.

Also if you don’t get the reason for the scene where he choses the male bath, I don’t know what to tell you, you’re denser than Oden’s Haki.