Yea, it’s going to be a problem if a lot of large instances start defederizing from each other. People aren’t going to want to have 4 different accounts to interact with communities they were contributing to before they defederized.
So instances with the policy to not defederate anybody (or other, clear and rather strictly open policies) become more attractive. Eventually, people who value open access will live on instances catered to that need.
The need for moving due to defederation or the need to have multiple accounts is only a thing during a transitional phase, I suppose.
Defederation happens much less often than new comments are posted. The visibility information is also the same for all comments, posts and communities on one instance.
So the check would not have to happen in real time for each comment. It can probably be done once per hour/day for the whole instance as a low priority task.
I like the idea of a visibility indicator.