I think there’s an element of “careful what you wish for” (hence my stance of “let it be”). I think the risks of over-zealous behaviour, defederation and apparently spontaneous loss of host servers is quite real.

Your idea of multi-communities seems sound; as long as the user is made aware of which community they are posting to when they reply (in case of quirks in the community rules etc) it should work - and over time it is likely that certain communities will become the “go to” for certain types of discussion.

Let it be. The duplication problem is all over the Fediverse. Over time some of those communities will die out and some will become more distinctive or specialised, attracting specific engagement in their own right; the problem will solve itself.

Have you disabled viewing posts from bot accounts? It’s one of the user settings.

If you have disabled viewing posts from bots, this is what you would see if a bot commented.

That’s my guess too.