To start with, "transgender" is an archaic phrase rarely used in the current UFP as no one currently distinguishes between those your time period consider to be transgender and cisgender.

There are, of course, many transgender Federation citizens, however early access to quality medical care, gender inclusive education and a non-biased legal system means that young people don't self-identify as transgender. No statistics are publicly kept as the number of people who transition after the age of majority are few, and the records of genetic transition surgery are sealed between doctor and patient. The ability to replicate and transplant even the most delicate of tissues means that for those who transition young there is no biological difference between "natural" males and females and their transgender counterparts.

Much more controversial within the Federation post-23rd Century was the existence of the transspeciest movement, where those sentients who claimed to be in actuality, transVulcan or transKlingon sought an end to the Federation ban on genetic manipulation arguing that cisspecies individuals had long enjoyed access to transitioning genetic manipulation and that plastic surgery was not enough to feel "whole" within their identifying species. Some groups identified themselves with GLBTQ movements of their home planets, particularly those transAndorians for whom four gendered biology often meant transition to an entirely different gender as well as species.