In my view, the New Yorker is an incredible publication that typically features writing that is superb and also well edited (if edited at all). So that's why this one stood out.
Maybe the issue is that so many people are quick to label anything that sounds like rationalism as alt-right.
I read the thing James Damore wrote and the problem was not the content he claimed was factual, it was the tone. He could have made the same point without sounding like he was on a "side" in an ongoing battle.
The elderly Richard Dawkins gets into political sides taking, as does Sam Harris. Both do little to hide their islamophobia. This appeals to those who were looking for scientific justifications of their beliefs, but also alienates anyone who wanted dispassionate science.
That is an issue, but I'll hope it's uncontroversial to point out that people like, say Curtis Yarvin, who are closely associated with both the alt-right and rationalist movements. There is in fact some significant overlap between those communities.