There is no reason to disbelieve the subjects of this potential story got the impression the story is going to be positive. This happens a lot and sometimes turns out to be inaccurate, it's at the center of lots of post-publication journalism kerfuffles. But we haven't seen the story. We haven't heard the journalist's description of any of these interactions. All we have are the impressions and recollections of one side.
It would be truly strange for the NYT to dox a pseudonymous blogger against their directly expressed wishes in a puff piece about that pseudonymous blogger. I believe that Scott Alexander believes that’s what’s was going to happen, but the motives just don’t line up.