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.