I'm not sure what Bluesky was attempting to do here but what they achieved in practice was allowing a user to claim control of a domain by claiming control of a page. But if you allow user generated content on the home page of your site, there's not a distinction (from a Mastodon user point of view) between the two. It's effectively the same problem if I can "verify" yourdomain.com on Mastodon - and my point is that you can do that without using .well-known.
If you allow UGC with *arbitrary HTML* or explicitly support generating rel=me. Both are you explicitly giving someone control of the site (or at least letting them claim they have it).