One time when I used online checkin it for some reason didn't take my credit card info via the website and therefore no room charge privileges on arrival. It absolutely wasn't a problem for them to add it and re-print my keys so there is certainly an element of flexibility there.
If you prefer to have your a choice of room on arrival then I'm not actually sure there's any benefit to online checkin for you. When you arrive, you show your ID, they turn around, pick up your folder and pre-printed keys that's already sitting there ready and then you head off to your room. It's super speedy.
In light of how easy it was to fix my room charging issue I'd say likely that it wouldn't be a problem if you then asked about other room options as normal however it does seem to negate the 'pick up your keys and go' concept as you're basically reverting to the normal style of check in.
Just my 2 cents