It's pretty easy to prove that a given domain was registered by a given registrar, so it's pretty easy to say that e.g. Hover is responsible for example.com, so

It's pretty easy to prove that a given domain was registered by a given registrar, so it's pretty easy to say that e.g. Hover is responsible for example.com, so Hover can request one (!) certificate for .example.com (or re-request it and revoke the old one). Then the only problem is when your registrar is a bad actor, and that's rough because they lose all* their business when people find out that they're screwing over their customers.