I think the article makes a strawman:
Academics hold tightly to the view that progress in our system is meritocratic. Hiring, decisions about article publication, citation of the work of our peers, the awarding of research funds, raises, promotions and more are determined, we believe, rationally, as a result of the objective evaluation of clearly stated requirements for advancement.
I don't think most academics think that either hiring decisions, publication decisions or citation decisions are 100% based on explicit criteria. Indeed anybody who doesn't use a variety of implicit criteria for decision making is a fool.
Smart people make hiring decisions often based on the predicted effect of the hiring decisions and not based on whether "requirements" are meet and a person did certain things in the past the fill checkboxes. Goodharts law makes the practice on hiring based on clearly stated criteria stupid.
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.