On our last trip we were upgraded at both resorts

No particular reason why I think it was due to overbooking....we were upgraded at Wilderness Lodge to concierge level due to overbooking, if we had checked in online our room would have been allocated and we would not have been offered the upgrade (I think it helped we are a couple and were moved into a king disabled room which would not have been suitable for families).
Posters on the resorts board are always saying the online check in limits your chances to get an upgrade for these reasons
So as I said before I would not do online check in unless I was in a value