What you don't seem to be getting, gbaji, is that this isn't just about one individual, but an entire minority.
I get that. But then we're also not talking about just this one school, or one class, but everyone who isn't transgender. Ultimately, we're looking at two groups with incompatible needs. One group's needs are no more irrational than the other, so doesn't it make more sense to inconvenience the smallest group possible?
And you're basically saying to them, "You make us uncomfortable and we don't like it. Go away and hide yourself, pretend you are someone else so we can continue to put our heads in the sand and pretend you don't exist."
The alternative is to tell everyone else "You make us uncomfortable and we don't like it. Go away and hide yourself, pretend you are someone else so we can continue to put our heads in the sand and pretend you don't exist." Can't you see that it's the same thing in either direction? Non transgendered folks are uncomfortable with someone of a different sex using the same restroom because they make that determination based on sex, while transgendered folks are uncomfortable using the restroom with people of the same sex because they make that determination based on gender identity instead.
Who wins? Is it any less fair to the non-transgendered folks to be forced to share a restroom with someone they feel uncomfortable with, than the other way around? Being in a minority group doesn't automatically make what you want the right choice.