Communities on different instances about the same topic should have the option to essentially federate so a post on one appears on all of them and opening any of them shows you the comments from all of them. This way when lemmy.world is down its not a big deal because posting to any news community federates to all of the communities instead of barely having people see your post. Federation could be decided by the community mods and the comments can have a little “/c/communityname@instance.name” on it so you know which community the comment was originally posted on.
Even thinking of it in terms of non-fediverse platforms. reddit often had multiple subreddits about the same exact topic. But the communities were different, often even splinters from each other because of disagreements on content and moderation. You end up with the original sub, Foo, followed by FooMemes, and TrueFoo, TrollFoo, FooJerk, etc.
If communities start getting merged together automatically, it’s going to end up causing problems. Most likely the culture of someplace like lemmy.ml will end up being marketedly different than some other instances (and already is). I would not want posts from a memes group there mixed with a memes group from elsewhere. Grouping the same post client side, sure. But there’s a reason for separate groups about the same topic.
I would say that it would work if communities could agree to federate because they believe their content and user base is similar enough to make sense, and splinter communities would not be federated because they are for different purposes.