They're different communities, just like /r/tech and /r/technology, /r/DnD and /r/dndnext, or the million different aita subs that popped up last month.

There is a GitHub issue for the Lemmy equivalent of a multireddit which would allow you to create a compound feed of several communities. Others have gone further and requested some kind of automatic merging, which strikes me as a pretty terrible idea... they're different communities with different rules and different mods and maybe different cultures. Sometimes they exist separately because the mods don't like each other or have very different ideas about what the culture should be. Transparent merging in such cases is awkward and creates confusion.

My advice is to consider the server name as if it were part of the sub/community name so that [[email protected]](/c/[email protected]) is just a different thing from [[email protected]](/c/[email protected]). Dupe subs have always been a thing on Reddit, they're a thing here too. They will get better with time as community discovery improves and people aggregate in the active/well-moderated ones and the abandoned ones die off.