If I were a transgendered person, hopefully I would be a good one and could "pass". Then I would quietly use the restroom I looked like I should use, without a bunch of defensiveness and nonsense, not making a big deal out of it to try and piss everyone off.
I have a female friend who is a lesbian, and she is also quite androgynous. She uses the ladies room, and to my knowledge nobody has questioned her or concerned themselves with her gender. I will bet, however, that she could also roll into a mens room and none of the guys would think twice about her being there because she looks very guyish and has guy mannerisms. I should ask her if she's ever used the mens room - some guys sit to tinkle, right?
Of course, when you're talking about bath houses and locker rooms, it's more apparent who is who and what is what. So my suggestion is that they simply adapt and deal with it, like someone with any other medical or mental problem does. Life is not set up to accommodate every single piddling difference people might have, so the person with the difference needs to figure out a way to deal. It's not our responsibility to deal with it for them, or be inconvenienced because of them.
While a woman wouldn't go into a mens shower to ogle the nekkid mens, men would absolutely try and get in to ogle the nekkid wimmins. You guys are a bunch of perverts and statistically WAY! more likely to be a sexual predator or child molester. So no, we do not want your stranger asses in our restrooms and showers and that's that.