Because literally the entire episode is basically "You will never be a real woman, no matter what". Perpetuating the that trans people getting gender affirming care don't know what they're doing and are just mutilating their bodies. There's literally a line where Garrison is talking to their doctor and says something along the lines of "Wait, so I'm basically just a dude with a fucked up dick?" and the doctor responding in the affirmative.

I genuinely really like a lot of stuff from Trey and Matt, but that's one of a couple times where it felt far less like "poking fun" and was intentionally portraying trans people in a harmful way, in a way that an episode like "The Cissie" didn't do nearly as aggressively.

I haven't watched it in probably 20 years (whenever those episodes came out, time is an illusion and lunch time doubly so), but wasn't that whole arc about Mr Garrison thinking they had to be a woman because they're attracted to men and therefore couldn't just be a gay man? Which seems more about old school homophobia or maybe the transphobic "trans women are just gay men trying to trick straight men into sleeping with them" autogynephelia thing. Plus there were all the usual Republican "I'm not 5ft 11! I'm trans 6 feet!", trans-species, and trans-race "jokes" that are transphobic. Those were basically 1 step removed from them making an "attack helicopter" joke (if that).

Also, this?

Garrison was trans, then wasn't

That's transphobic. Being trans isn't any more of a choice than being gay. Kissing the homies goodnight with full tongue isn't you deciding to be gay for a day and then deciding to be straight again, and experimenting with your gender isn't waking up one morning and deciding to be trans for a day.

You may try it and decide that it isn't for you, but that doesn't mean that you were trans or gay and now aren't anymore. It just means that you ran an experiment that helped you learn more about yourself.

And to go further, breaking gender stereotypes (like femboys do, for example) doesn't make you trans either, but it does make you cool for being brave enough to give the finger to society by not playing the stereotype they expect you to play. And if you try it and decide you don't like it? That's cool too, you were brave enough to step outside your comfort zone and the rules society wants to force you into in order to try something new.