Please don't think this is insensitive, these are legit questions I have (and like oldguy said, I didn't even know some of the topics in this thread were actual topics, so kudos), and I'll use a real-life public figure as an example...
Chelsea Manning (I'm pretty sure) has the body that is physically male, XY chromosomes, etc. She has now asked to be identified as a woman, changed her name, and desires treatments/surgeries/whatever to make that happen. Fair enough.
Pre-name change, Private Bradley Manning (I assume) had the same desires/thoughts/feelings/"gender leanings" that Chelsea does now. Would it have been legal and/or appropriate for Private Bradley Manning to have been using the women's bathroom, showering with women, living in the women's barracks because he identified as a woman gender-ally, vice being male physically? Or was it an infringement on his rights to make him do the same with the physically male?
I ask because there doesn't seem to be a way to reconcile it--either it's an infringement on the rights of the trans-person to be forced to utilize the facilities that they physically identify with, rather than how they identify gender-ally; or you do away with physical male/physical female segregation and segregate by gender identification (sexual identification?), which seems to be a "separate but equal" issue waiting to come up.
Put another way, I personally would feel as uncomfortable with a physical female (who identified with male) taking a shower next to be in the gym, on the submarine, etc. Chelsea Manning (even knowing her sexuality, how she identifies, etc) taking a shower next to me would not be an issue. Would you say that's just bigotry on my part? Is that something that society should be cleansed of? And (not legally, but societally) are we all comfortable with physical males able to walk into women's showers without question, and assume that they are there with good intentions because they identify with being a female, vice being a predator? Again, just mho, but I tend to error on the side of protecting women, because I don't believe in the inherent goodness of individuals.