So what? The story isn't about who Scott Alexander is. The story is about the blog. Anyone can go to the website and read the blog (or at least they could before the NYT pulled this screwup). If the NYT wants their story about the blog to be credible, they just need to tell the truth about what the blog says.
It's about the blog and its author. It's like writing about a controversial book without any mention of the author. That's not possible.
The author's persona on the blog, yes. That doesn't mean the author's real name needs to be revealed.
> A Warning is a 2019 book-length exposé of the Trump administration, anonymously authored by someone described as a "senior Trump administration official". It is a follow-up to an anonymous op-ed published by the New York Times in September 2018.