They made fun of people with suicidal thoughts and the perception that others have about suicide, all in the same series of episodes. Compared to that, making fun of trans people shares many similarities, so naturally, trans people are not above the acceptable threshold the show has, if they even have such a thing as a "threshold". That is what makes the show work in the first place. Could you imagine if a show all about being politically incorrect suddenly had tight morals..? That is an oxymoron and a half.

If anything, I find it weird that they never made fun of some low-hanging fruit groups like bronies or furries at any point. A lot of people assumed they would eventually. Like, hell, they mocked Yaoi fans already, so I doubt they are unaware of internet subcultures like those. Where is my episode with Cartman talking shit about me for liking Sonic with every possible strawman in the book..? I also want to be insulted by a cartoon, damn it.

Maybe they didn't do it BECAUSE it's such low-hanging fruit.