Regarding the fediverse at large...
I believe that this is a design issue. Instances are designed so that they function like categories. That categories then have subcategories.
The issue is that with user distribution, you can't then just assign users round robin distribute the load. This leads to what we now have which is very confusing to the end user.
Users was a centralized experience. The duplication of communities is a prime example of the bad design.
In the abstract, I would consider putting all instances in a pool. Each instance runs a different community, with servers also duplicating x number of communities for the sake of redundancy (instance goes offline, content still exists on another server). It's complicated, and has it's own issues/flaws, but I believe that from a high level view, it is a better design in general.
The current system is just a mess unfortunately.
Perhaps there could be a hybrid of these two approaches that would be superior.
My back of the napkin design prioritizes user experience and ease of use. That said, I can immediately think of a few downsides.