I kinda see your point, but I think context is important here. For many trans people, part of transitioning includes working toward presenting as their identified gender, and that process can take time and effort. So when someone says "you look good for a trans man/woman", in a clumsy way, it might be meant as recognition of that effort, like saying, “you look exactly how you hoped to". Which is completely different from automatically assuming that all women are stupid for being women.

“Yeah, you’re pretty good lookin’, for a girl.”

Sorry that I neglected your comment, but my response to the neighboring comment applies here as well.