If your issue is that an online handle may sound strange or silly (e.g., ‘Count Dankula’), how would you handle someone whose legal name sounds strange or silly (e.g., ‘Moon Unit Zappa’ or ‘X AE A-XII’)?

If your issue is that an online handle is not someone's legal name, how would you handle someone who goes by a certain form of their legal name (e.g., using their middle name rather than their first name)? How would you handle someone whose name includes a title (e.g., ‘Cpl Bloggs’ or ‘Ambassador Taylor’)?

Everyone has a number of labels used to identify them, and the appropriateness of each is dependent on the situation being used. In the context of an article about the online community surrounding someone's online blog, which they publish under a certain name, it is entirely appropriate to use the relevant name. The only way that that person's legal name would be relevant to the article would be if it was reporting on their conduct outside of that community as well, which this article does not appear to have been doing.

Scott Alexander is actually his real first and middle name. All he’s asking is for them to not use his real last name. Apparently, that’s beyond them, they simply must do it regardless of the cost to him and of how little relevance it has.

Really? "A popular blogger who writes under the name Scott Alexander…" isn't really any worse than "A popular streamer who uses the handle Day9" or something.