I dunno. I tend to see the Trek world as pretty much akin to Iain Banks's Culture series in regards to gender. Gender reassignment is simple and reversible, so people often switch back and forth over the course of their life just because they feel like it. Hell, I identify as 100% cis male, but if I could step into a doctors' office for a few hours, come out looking exactly as I would have if I was born with a female body, and could switch back at any time, I assuredly would have tried out being a woman for at least awhile in my 20s to see what it was like. And I'm not even the product of a 23rd/24th century culture, where I presume transphobia is dead.
Regardless, as I said in my first post, I said that more aptly trans status wouldn't be salient. Trans status became a salient point of identity because we live in a transphobic culture. If we lived in a culture without transphobia, it might be accorded as little import as being left handed or having blue eyes.
Of course, Trek has never really been meant to be an accurate depiction of what the far future would be like, but to provide a mirror on contemporary issues. To the extent that this is true I absolutely agree there should be a trans depiction in Trek.
The question is though, how to depict it? I mean, presuming transphobia is dead, you'd basically just see an actor/actress who at some point showed some holos of themselves as a child presenting as the other gender, and then an "oh yeah..." and then it would be dropped entirely. To deal with the complexities of trans issues, you'd probably have to have an alien or splinter human culture who was transphobic to contrast the Federation's acceptance with the condemnation of the othered culture of the week.