Seems the easiest solution to that would be to simply have a comparison view. The permissions are setup using some sort of sta.dardized method, yes? Config file, GUI, whatever. Certainly it wouldn't be hard to simply grab and organize a list of perms from both instances and toss em up side by side. Could even add notes (i.e. if photo storage on Instance A > Instance B notify use "migrating to this instance may cause some larger photos to be removed from your account").
I'm not a professional programmer (sys admin, so mostly just automation) but there are certainly solutions to this.
What you're describing is one of the root issues with the current system. It's the same reason that if your instance goes down, your account and history go with it. I'd love to see an implementation of some sort of account awareness like you said, which could also make it easier to backup history to another instance in the event that your primary goes down.