Frankly, I think you might be giving Gaiman too much credit as a writer. I know that he has a cult following, but I have found his work to be shallow and not particularly thoughtful. Gender essentialism seems right up his alley, in my opinion.

Of course, one can be a gender essentialist and still have the decency to realize that even people who don't agree with you are people, and not freaks and monsters. Perhaps that is what is coming across in that story, which has always itched at me as well.

I agree with Argentla above that the pregnancy side of that whole plot -- the way the female character in that case was trivialized to the point of near non-existence -- was infuriating. I also found it stupid and not well put together.

I'm not familiar with "The Invisibles," so I can't make a comparison myself.