Agreed. It usually means a manual change to the reservation. Which I equate to Upgrade. Happens with both prepaid and flexible/AAA rates.

Although sometimes the upgraded room is visible online.

The benefit is that I can change dates/rates or cancel if need be, if it's done "in the system" but otherwise it requires a call to perform these activities.

It may also have something to do with the level of IT integration between the hotel and ICHG? My guess (totally unconfirmed/unresearched) is that the hotels where you can see your bill online also show you your upgraded status online,while those that don't, don't.