I think this is currently one of the biggest problem of Lemmy on the UX department. Non technical users from Reddit will only expect one "subreddit" for a theme, but if they search on Lemmy, they'll find more than one community with the same topic, and it'll confuse them and make them less likely to come back.
But that's the way how Fediverse work, so I don't think combining two communities should be done from the Fediverse side, but rather each Lemmy instance can curate a "playlist" or "multireddit" that has some of the biggest communities from the users' server and other federated servers about the same topic, and users can subscribe to the "playlist" rather than individual community.