Keeping communities separate is the simplest way to go, tbh. Sharing karma could lead to weird brigades, like r/ScreenshotsAreHard cross-posting from every picture of screens on the Fediverse and then mass-downvoting from there.

To me, the best solution would be to implement multireddits. That way, you can have your cat multilemmy of 100 communities without affecting your main feed, but you could also do the same for related or identical communities. Plus, moderators could create a multilemmy and display it prominently in their sidebar.

Being able to subscribe to a multi would solve that issue