not saying they are trans, but denying it because they said "i'm not a girl" instead of proving their aren't trans, just proves you don't know about trans people xD
it's one of the most common things to deny ur gender when ur trans, there are a gazillon memes about that lol.
but yeah, this manga doesn't set anything in stone and I think that's also nice sometimes, it could resonate with crossdressers, trans girls, guys who just want to look cute.
it's part of the charm~