People talk about duplicate communities in the Fediverse as if it's a new problem. Reddit has loads of these though - it's not unique to the Fediverse. What happened on Reddit is that the communities in question eventually settled on one subreddit being the 'main' one for their community and then most of the traffic ended up with those ones.
There is no main community. Different instances see different posts so some users may not even be aware of some communities. Or they may be subscribed to the largest community for a topic but because of federation wonkiness they don't see all the posts in a community.