It's difficult
Int think there should be expenditure to make a third non-binary changing room and allow trans pupils to use either bathroom depending on what they feel is the best for the school be it identity for the pupil or biological sex for ease while allowing all gender based necessities at that point, because a trans woman can use a male bathroom and only use stalls but I see how they could not like that but they capsule also change in the males into the female uniform and go to female PE classes again for child protection laws as they forbid opposite SEXES to change in one room not gender, again very difficult but I think that the uniform issue just needs to break down out of gender identity like one school here in England did was rename them to trousers and skirt uniforms, in my academy it would be business dress without added male and female before or after it, by coming this it means girls can freelay wear the "male" uniform as many do as they prefer it but it also allows the smaller minority of those with gender disparages and cross-dressing gender issues to do as they please too. Very complicated but most Trans friends of mine say they are willing to put up with biological bathrooms untill they fully present the correct sex or have transitioned, there's always stalls so no one will need to know. But I think you are thinking a bit to nicely as many people still don't like transgender-ness but I agree as adding a "trans" option defeats the point of trans really and is going over PC, remember a lot of trans people are mentally tough enough to stand not having the correct bathroom because they have faced so much already it doesn't really match up.
I've rambled the main point is, don't treat them special that's the opposite of what they want and most these things are based off of biological sex by law through child protection