DH travels for work, and we book all his hotels through hotels.com. There has only been a small handful of hotels that's cruddy enough to put him in rotten rooms. And half of those times there has actually been something wrong with those rooms (A/C out in Singapore, for example), he complained, and was moved to either a more normal room in the class he booked, or he's been upgraded.
I can't say if Disneyworld would or would not upgrade simply based on where they booked, but it didn't happen to us.
Not only did we book through hotels.com at POR in Feb, but we used "free" nights, which means we paid something like $50 out of pocket (along with losing two "free" nights of course) for our Royal Riverview room.
We got 2nd floor, far corner room Parterre Place. Gorgeous room, quiet location, fabulous.
I was able to get the proper 12 number Disney confirmation number by asking hotels.com, and then I was able to put that into the disneyworld website. It never showed up *right* though; it had me with my last name, then it had "Unknown Molly'slastname" for both DH and DS. At actual checkin we had to fix that and we had to put in CC information, as online checkin had lost that.
Also, even though I put it in with their 12 digit number, later on that number went away, and I saw a different, shorter, confirmation number on WDW's website, for that reservation.
I was able to do nicely early checkin (I was doing all that after they showed the 60 day checkin, but way closer to normal checkin than 60 days, simply because there weren't 60 days between that going "live" and my trip), which was important because we were arriving after 1am. I was able to request a corner room on the checkin form online.
And as I mentioned, we got it, despite booking for SO cheap and arriving SO late. I don't feel we were punished at all for booking through hotels.com.