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One thing they never really get into in Star Trek is how the body modification scene evolved in a future with medical replicators and "Doc will shine a light on it" levels of medical technology. I'm sure they could easily perform a gender transition, including changing reproductive organs to whatever combo a person wanted, in an afternoon, to say nothing of the possibility of cosmetic and functional structural changes. We see them perform highly complex and detailed biological modifications so crew members can pass as aliens like it's nothing, so why not make people taller/shorter, wider/narrower hips, bigger/smaller boobs, more feminine/masculine face, horns, pointed or alien ears, new sense organs, extra arms, etc. What kind of wild piercings are people getting? What new methods and styles of tattoos have they come up with? The possibilities are incredible. That would be a fun world to explore, even within the Federation's taboo against genetic alteration.
Everyone would request the ability to suck their own dicks, and never leave the home anymore.
I think playing with the body and especially the mind (through eugenics, genetic engineering, or any other means) is as big of a nono in the Star Trek universe as fascism, due to trauma from the eugenic wars (you know, when Khan and his ilk fought baseline humanity).
Body modification enthusiasts, transhumanists, furries, and anything like that are probably treated with fear, loathing, and disgust.
Heck, they won't even treat baldness despite being perfectly able to fix it if they wanted to, and they don't seem to have made any effort to cure aging, despite being able to cure almost everything else; their life expectancy isn't much higher than ours, when it should be much higher.
You want that kind of thing try Iain M. Banks' Culture series. Even more freedom to live your life however you want, the only limits to body modification are your imagination and some of the laws of physics (much less than in Start Trek, though), and people live to a healthy 300 or so, throw a party, and die in their own terms because they're done, or curious. Or do not, no one is forcing them, they can keep on living if they want to.
Heck, one character used to have about sixty penises all over his body, just for fun. No more, though, even with four hearts at that point it was starting to get difficult to maintain an erection at the same time in all of them.
Quark gets a gender transition on Deep Space Nine
Oh yeah that's right I forgot about that. He got a full gender transition in a couple hours.