I think you've missed the point. The point is that even if Scott were in fact a conglomerate of twenty people, Scott's writing is still the same, and is what draws people to the blog, and is ultimately why there's any story to be written at all. Nobody, but nobody, cares about the actual human originator(s) of the posts; it's the persona who matters.
Agreed, the author who writes under a pseudonym to protect himself should definitely be part of the story. We definitly talk about Scott Alexander, the pseudonumn everyone knows to be connected to the blog.
I'm not sure why though, the NYT, would need to know the name that is purposely never used.
If you really need the name sooo bad, then just don't dox him and drop the article. That's perfectly fine.
As long as they don't dox him everyone is cool.
If they can't write the article without doxxing him then they should just drop the article.
Whatever they do they shouldn't dox him. And if they can't write the article without doing so, then they shouldn't write it.
Ah, I see you're from a different culture to me. I gave up reading anything that looks like mainstream news, and am much happier for it, in part because I wholeheartedly disagree with the mainstream news's founding sentiment which you summarise as "and that's important".