I don't even think it's a difference with Reddit. Reddit also has community duplication. Sure, maybe not as bad, but it's there. Compare /r/meirl to /r/me_irl. The only difference is that in Fediverse you'll see the same community name in different instances, but is it really that much more confusing than the meirl case?
There is, yes, a lack of discoverability for communities. Maybe we need a "recommend me a community" community. Like "I'm looking for a Spanish speaking science fiction community", and people can say "oh, yeah, try this one".
Other than that, the main advantage Reddit has in this area is that it has had a more or less stable population for a very long time, so which community wins out out of an initial set has already been resolved, while this is younger (yes, it's been around for a couple of years, but most people here haven't) and therefore that process is just starting to play out.