I think rather than continuing to debate relatively peripheral issues (such as consistency or the culture of psychiatrists), let me just state what I think the crux of the issue is:

I believe that journalists ought to honour all requests for pseudonymity, unless they believe there is a strong public interest in not doing so in any particular case, and if they believe there is such a strong public interest, they should be explicit about what they think it is, so others can judge their public interest claim. I think this is the decent thing to do, and sustains a culture of respecting people's privacy.

NYT did not follow that standard in the case of Scott Alexander.