It's awkward for me because the comment feed feels very segmented. It's awkward to have a big header for a smaller/niche instance and one comment below it.

It makes that comment seem like an orphan and gives prominence to people who use the biggest instance.

I'd also want the sort I apply (Hot/New/etc) to apply to every comment, not per instance.

I'd propose something like this.

Clicking on the Server dropdown could be a simple checkbox group, which would remember your configuration across that instance. That way, if you wanted to hide specific communities from appearing, you could.