@evan There's a lot of tools -- including a somewhat crappy one that I wrote -- that try to recommend instances for new users who don't know where to register, for one example. The way mine works is by querying instance stats so it can see if registrations are open, what types of media or post lengths are supported, language, user counts, etc. So if users start bringing their own domains I either get my DB cluttered with fake single-user instances or I end up giving someone two dozen suggestions that are actually all the same server. And I'm sure I'm not the only person who has code that will need to be redesigned if that one domain per instance requirement gets broken. And it's a reasonable assumption to make if you're focused on Mastodon, since its configuration files (.env.production) only allow a single domain to be specified.
You could just use it as an alias though:
https://guide.expressional.social/guide/use-your-own-domain/