When you check in online, you still have to check-in with a cast member when you arrive at the resort so you still have the opportunity to ask for a different room location. Online check-in just expedites the check-in process, it doesn't eliminate it. We do online check in all of the time and if I don't like my room location (which happened only once), simply ask if they have another room. We went to AoA in June and when I booked, they only had Cars left and we really wanted Nemo. When we arrived, I simply asked if there was anything available in the Nemo section. The CM checked, there was availability, so she re-assigned our room.
My suggestion, call in your room requests to CRO, do online check-in, ask to change your room at check-in if you don't like it.
Your room is assigned days before you arrive, whether you check-in online or in person. Simply by checking in online doesn't lock in your room assignment - you can always ask for it to be changed.