Why “refer” to them at all? I don’t see the issue. When we determined that a fellow student was a fruitcake, we just ignored them completely, no need to worry about what they wanted to be called, that particular day.
They could have been mocking her, instead of ignoring. Deliberately saying things in her hearing, like, “Lee used the boys’ room, can SHE piss standing up or does SHE still sit down?”
And I think a thousand to one, this girl is a social contagion transgender unhappy child with other problems, and she doesn’t belong in the boys’ room.
Way around it all, just refer to students by last name only.