Which he did not say. The discussion on gender differences was providing possible reasons why women may be less likely than men to pursue engineering careers. It says nothing about the relative ability of women who do choose that path.

I didn't see that at all. What I understood him to be saying was that on average (across society), there are various biological differences. I don't see any insult there, intended or not.

I thought his only intent was to argue against institutionalized discrimination.

It was.

Apparently, lots of people either haven't read the "manifesto", or have but have read into it something not explicitly stated by the author.

I think some critics have claimed that the things explicitly stated by the author implictly mean something bad, but they haven't actually made the effort of showing that conclusion is supported by anything the author wrote.