You're concerns are a remnant of a binary gender culture anyways, it's just so much more complicated than that. What about a girl that likes girls? Or a guy that is now a girl that likes girls but still has a penis that can get hard? The possibilities are endless.
With the gender revolution the one thing we have come away with, is that sex and gender apparently is subjective and labels do not apply. As such, just do away with it, and get over it.
So you are saying that we should just have one high school locker room and all the kids should just change together? Yeah, I don't think that's going to ever fly. Same thing in the adult world, despite being able to save money I don't see them going to a single locker room anytime even remotely soon.