I'm going to throw Eclipse Phase a bone here and say that because the setting indicated that bodies are pricey, I can see legitimate scenarios for transgenderism. Specifically, person low on cash can only afford a "slightly-used" body, body is a different sex from what the person's born as, now they're stuck in it until they can afford to swap it out, bam, valid in-game situation for there to be a transgender character.
The thing is, that character should be viewing their situation much like a person today who bought a used car that turned out to be a lemon: An annoyance that will be rectified as soon as means allow. They wouldn't have all of the identity baggage that comes along with 2020 transgender people, because the fix for their problem is obvious and straightforward by the standards of the setting.
My bigger beef with the setting is, like other people mentioned, the way it tries to portray the Jovians as being crazed in their dislike of technology after out of control technology went and murdered like 99% of humanity. And their very valid fear that copying yourself into a new body isn't actually copying "you", but making a software duplicate of yourself who walks around and acts like you.