I think anyone who is not a sociopath would consider this proof of a “substantial risk of harm”.
I wouldn't be opposed to the story running under a fictional name, even though that would probably not be to Scott's liking either.
In the specific case though, given a really well established pseudonymous online identity, that is the central subject of the article, the marginal utility of the additional information you can check seems uniquely low. At least if the subject is just the pseudonymous activity of the author.
At the point where the NY Times is reaching out to write an article about you, I think you have likely crossed that threshold. Scott's best move would have been to refuse an interview in the hopes that it would kill the story. But even that might not have mattered. If your goal is to be both famous/influential and pseudonymous, you probably need to work a little harder to protect your anonymity.