tl;dr: I agree with OP that the ability to have multiple, identically named, disconnected communities on different instances will be a severe detriment to the adoption of the Fediverse by the general public.

community names are already globally unique and multiple identically named communities cannot exist, you’re just not looking at the full name.

That's part of the problem. The simplest UI generally exposes the community name without the instance, !memes for example, but the backend is really !memes@lemmy.ml which is an entirely different community from !memes@sopuli.xyz. Now, that's not really a problem - memes are memes. But what about a community for Edinburgh, UK? There are already two - !Edinburgh@sh.itjust.works and !Edinburgh@feddit.uk. That's going to be an issue because if you choose one to participate in, you'll miss all of the content in the other. If you're a member of, say sopuli.xyz, you won't even know that either exist because their community search doesn't actually search all instances and might start a third. The whole idea of the Fediverse is to have a federation of instances which share information, and there is already talk of the biggest instances potentially creating a problem with the democratic ideals of the system (6 days into the reddit migration and three of the largest instances have defederated from one another). To have a thousand instances each with their own !Photography or !ManchesterUnited community dilutes the content and interaction.

I agree with OP ( I actually don't know how to link to a profile yet or I'd tag @TerryMatthews) that there should be some cross-linked mechanism to merge identically named communities across instances. There could still be detached instances - defederated content would not have their content propagated - but the content for each unique community would be co-mingled.

I would expect that moderators would be limited in scope to their own communities. So a mod from feddit.uk could block a non-instance post or user on their instance but it would be present on other instances. They could also block a local post on their instance and it would not be propagated at all. Pinned posts get a little more hairy - would every mod have a separate set of local instance pins? I would think that would need to be the case. The issue of sidebars is also an issue.