Communities on different instances about the same topic should have the option to essentially federate so a post on one appears on all of them and opening any of them shows you the comments from all of them. This way when lemmy.world is down its not a big deal because posting to any news community federates to all of the communities instead of barely having people see your post. Federation could be decided by the community mods and the comments can have a little “/c/communityname@instance.name” on it so you know which community the comment was originally posted on.
That system makes the instance a single-point-of-failure for the whole community, which has been a big problem lately. If communities could easily be multi-instance they would have redundancy. That seems like a good reason to me.
While I agree there should be functionality to propagate changes to a community between instances when the host is offline, there is no practical way to share administrative control of a community. Any decision by an administrator to sanction a community or defederate an instance will just result in exactly the fragmentation you fear.
The real solution is for small groups of communities with similar interests to gather on separate instances with few or no users. Meanwhile, other instances gather users with few or no local communities. This maximizes the benefits of cacheing community content while minimizing the impact of defederation. If a community host can no longer be maintained by its owner, that ownership can be easily transferred without transferring the burden of hosting hundreds of communities or supporting user logins.