Farscape is a deep cut.

Even Sillier than that is a British comedy called “Red Dwarf” and as far as I recall there is no transphobia. The closest I remember is an episode where the main character ends up in an alternate dimension with the female version of himself. They hit it off and the male main character of the series ends up pregnant, to his distress. At the time I remember it being a really interesting way to bring up gender dynamics without being too laboring, though it’s been a while, and I also haven’t seen the new seasons they apparently made after the show got cult status.

Edit to add: a Reddit thread has this to say about Red Dwarf and being trans

In series 8, Kryten is assigned to women’s prison wing, just because he doesn’t have a penis when he clearly resembles a male, sounds like a male and acts like a male. That’s regardless of the fact that he has no chromosomes because he’s an android (not even gynoid, so another good point). The show makes it out as ridiculous that the only reason why he’s treated as female only because of his lack of penis.

Also, in the episode DNA, it’s shown that when he’s turned into human male, he’s still an android on the inside because he clearly feels discomfort from certain dysphoria, where he finds appliances sexually attractive and inability to adjust to human biology lacking robotic features.

Edit to add to the edit, I forgot the ships on board computer actually does upgrade themselves to present female