I think they should have somewhere to go that is gender neutral, but most schools are underfunded and spending money on another bathroom facility maybe isnt necessary if there is a disabled toilet which is multi-sex anyway.
It is sad to see that there is still so much hate towards transgender people.
Based on gender views... The toilets should remain 'male' and 'female' as even though some people are gender neutral... A girl would not feel comfortable in a toilet whilst another guy is doing his business in the cubicle next to hers... This is a question of privacy not people's opinions.
I think the easiest way would be to relabel "disabled" toilet as "accessible" toilet - it's then there for anyone who, for whatever reason, can't use the gendered ones.