This has nothing to do with federation, reddit was a single system and had the exact same issue. It's simply a result of having communities that overlap in topics, or articles that are relevant for multiple communities.

The key is that each of these posts has a different discussion due to the different community it is in, isn't that good?

Absolutely, I've done more posting/commenting/upvoting in the last days than I've done on reddit in the last year.