I went and read the sequel and it opens with Kokuyou praying at a shrine to become a girl, getting upset that Shiro becomes a girl instead, and repeatedly states that they wish they were a girl throughout the currently translated 3 chapters.
You could probably point out that they refer to themselves as a boy when rejecting someone else but I take that more as a statement of “I’m a biological male, are you okay with that,” rather than just “I’m a boy.”
I dunno, it’s just how many times does a character need to say “I wish I was a girl” before we start questioning things anyways.