I wonder how much "positive representation" there needs to be before someone can make a trans villain* again.
I mean, some would be nice.
But most stories with "trans representation" will only have a single token trans character, and even if that's not true there will likely only be one trans character who is actually significant to the story. If there's only one significant trans character, then that character shoulders the entire burden of representation. If in every single one of these stories the only way people can imagine that trans character is as a villain, then that says something quite unpleasant.
There's also the issue that a lot of trans villains play on negative stereotypes about trans people. The most common trans villain is in detective or crime stories, and they're usually unstable violent murderers acting out of some perverse or misguided sexual impulse. The implication is always that them being trans is a perversion, or a part of their disordered mind which drives them to be a murderer. Usually if they're portrayed in film, they're played by cis actors. Their appearance is often played for laughs or gross out factor, or they're shown as creepy and weird and disgusting.
Basically, if your definition of a trans villain is a creepy, predatory, sexually deranged monster who murders people, you're probably gonna get some pushback for that. Especially if that's the only significant trans character in your story.
Trill are symbiotic life forms - Jadzia did not identify as male - she just shared their memories. Though that may have given her marriage to Worf some spice.
I will give you the TNG episode, as bone headed as some of the execution was that was a character whom wished to express and identity contrary to the one they currently had.
At the time, Star Trek was run by Rick Berman, who absolutely vetoed any suggestion of putting gay characters or subtext in the show (although he may also have been under pressure from affiliates). Anything which slipped through basically had to be hidden from him by the writers and cast.
The trans subtext in these characters and episodes is, I believe, an accident result of the cast and crew trying to sneak gay stuff in without making it too obvious. The Outsider , for example, is ultimately a story about conversion therapy with a heterosexual romance between characters played by male and female actors. We only read it is as a trans story because it's so mangled that its original intent is lost.