You can do online check-in without making any room requests. I did the TP room request fax for our trip in June and I did indicate 2 room requests on our online check-in as well but they were in line with our room request through TP. I chose 1st floor, near transportation when I did the online check-in. The specific room/location we requested on the TP fax was first floor and near transportation. If I couldn't have listed the same requests, I wouldn't have chosen anything on the Disney online check-in. FWIW, we got the location we requested -- actually the room right next to the specific one I requested but that was fine as I really just wanted to be in a specific hallway, I didn't care if I was in the specific room.
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