The "duplicate" communities are housed on different websites. Websites that could very well have their own norms, rules, and culture. Lumping them together and treating them as the same thing is just kind of invasive to them, and promotes bad netiquette.
Just pick one that you like best.
This sounds like the sort of thing that's best solved with a 'favourite' option that pushes posts from favourited communities to the top of the feed. No need to get in there and over-complicate it with bespoke weightings or anything.