I'm not sure this qualifies as first-hand experience or not. But, I used to work at the Disney Reservations Center (DRC) as a Reservations Sales Agent and a Facilitator (Disney-speak for Trainer). That was a number of years ago. Still, I can't imagine that anything related to this has changed.
Based on that experience, we always told guests that if they wanted to guarantee an early arrival, just pay for the room the night prior. The standard in the hotel industry is that the room is held for you up until the official check-out time. So, you should be fine until that time.
Regardless, if you don't arrive by the time the system resets (somewhere in the dead of night), you will get entered as a "no-show". But, as flortlebap notes, that's easily fixed.
This scenario isn't unusual. Any DRC Cast Member that's been working for a few months will have handled this issue before. I'd highly recommend calling to make this reservation instead of doing it online and then calling to have notes added. If I remember correctly, it's easier to enter notes while the reservation is first made than it is to add them afterward.