If so, could you sketch for me roughly what these differences are and how they lead to that result?
Let's see: there are numerous ones the most relevant are: women have less variation in intelligence then men and so there fewer unusually smart women. Women are worse at taking criticism. There is also a lot of stuff about the kind of hierarchies men and women tend to form.
Because I'm having real trouble thinking of any hypothesis of this sort that's consistent with what I think I've observed of the relative abilities of men and women.
Have you actually been observing the relative abilities between men and women, or is your reaction whenever you notice a woman doing something badly or acting emotionally to hit yourself for having a "sexist" thought?
women have less variation in intelligence than men
That could indeed (if the numbers work out) explain a difference in success at the very highest levels in the absence of prejudice. But this sort of effect is far weaker away from the very tails of the distribution, and the particular study we're taking as an example in this discussion is not concerned with the very tails of the distribution. Further, my understanding is that GRE scores correlate somewhat better with intelligence than they do with job performance (see, e.g., this post which has a few ref...
I remember seeing a talk of the concept of privilege show up in the discussion thread on contrarian views.
Some discussion got started from "Feminism is a good thing. Privilege is real."
This is an article that presents some of those ideas in a way that might be approachable for LW.
http://curt-rice.com/quotas-microaggression-and-meritocracy/
One of the ideas I take out of this is that these issues can be examined as the result of unconscious cognitive bias. IE sexism isn't the result of any conscious thought, but can be the result as a failure mode where we don't rationality correctly in these social situations.
Of course a broad view of these issues exist, and many people have different ways of looking at these issues, but I think it would be good to focus on the case presented in this article rather than your other associations.