You're right on that part. Federations works great with mastodon and its instances made of individuals directly interacting with each other's accounts.
But when it comes to interacting though communities already spread through instances, not only it makes it hard for people to follow all these duplicates, but it threatens the very principle of federation in a certain way. Because most people will eventually subscribe to the biggest community for each subject (tech, nature, photo), which often turns out to be hosted on the biggest instances...and that is centralization once again.
A solution could be for users to gather all the communities they subscribed to around topics. Then your feed would be a mix of these topics' groups and singles /c. Twitter does that similarly with its List feature.