Couple points, then I'll push away from the table.
1. If this actually happens - ambiguous gender individuals switching lockers/bathrooms/whatever - the qualities of the social lives of such individuals will deteriorate catastrophically. Enough girls (or boys) will refuse to be in vulnerable/exposed settings with them that I think it's more than likely that EVERYBODY will refuse. Then what have you accomplished? Your transgender kid gets a giant locker room to him/herself, and the rest of the student body gets a HUGE resentment. They're gonna enjoy living with that.

You've taken a tough situation and, by trying to be merciful and helpfull, made it exponentially worse. Watch. if this happens in a few places, and the ostracisation [sic?] DOESN'T make the news, meet me back at this thread and tell me I was wrong.
2. I don't care what the DSM or goaliemn or or the AMA say. These kids are not disordered. You've used that word over and over again. Ambiguous gender births are pretty common. More parents than we realize have been called into a waiting room and gently told they get to choose.
3. You keep talking about making accomodations for other disorders (again, I don't agree wth that word here). What you fail to see is that those accomodations work both ways. No student has the right to interfere with my kid's education. If littel ADD Alice can't shut up in class, she needs to have an aid who pulls her out so my kid can learn. If EBD Johny is violent on the playground, he needs to go. FAPE says he gets to have the same OR EQUIVALENT recess/excercise opportunity as the other kids. LRE says that we'll try it with the group first, but if that's not gonna work, it AIN'T the other kids (and their parents) problem. He can play with his aid and/or the other EBD kids in a different place until he proves he can fit in. Again, the rights of the individual end where the rights of another begin.