The ghost cards would work exactly like they do know where they are tied to a core set. When that core set exits Modern, for example, the ghost cards for that set exit as well. Everything is already programmed this way so not additional work in that area.
The system would also assume the highest level between player owned and ghost card, again like it already does. Until they make the card selecting more universal to allow for picking certain levels if you have them available, I don't see why this would change until then.