That's the way federation should work, but it doesn't currently work like that.

I would dispute that, actually. Sometimes people make separate communities because they want there to be separate communities. Over on Reddit that required you to make communities with different names, but here you can also do it by going to different instances. Maybe there's a startrek@lemmygrad.ml that's all about how awesome the Romulans are, and startrek@startrek.website wants nothing to do with them.

There's a reason people tend not to use those small forums anymore, and favor larger sites like Reddit.

If that's the case then your "problem" will be self-correcting, if there are multiple threads on the same subject in different communities people will tend to contribute to the larger one and it'll snowball at the expense of the others.

Some people might prefer the smaller communities and threads, though, and thanks to federation they can pick whichever one they want.