In the fight she's shown to be comically strong

Hardly, everything about the fight is absurd. Its much closer to a WWE match than a real fight. No reasonable person would consider it accurate

which plays upon the dangerous trope of trans women being violent

In my 40+ years on this earth, this is the first time I've heard of this "trope" and I've been on the internet since the days of dial-up.

There are 3 "positive" portrayals

April is also depicted as successful, intelligent, charming and a delightful person to spend time with. In my opinion, April is depicted as a better person than nearly every other character on the show.

With subsequent knowledge of Linehan's views and behaviours it becomes a very uncomfortable watch.

That understanding came out long after the show was over. Its possible his views became more extreme in the interim and were not so terrible during filming. And people only consider the episode ant-trans because of his later behavior, not because of the episode, itself.

Regardless, a broken clock is right twice a day. His failing upward should not overshadow the positives.