Please be aware that how those hotels operated doesn't mean that every other hotel operates in the same manner.

For example, I once worked for a hotel company that did not use the origin of reservation as a factor when assigning rooms. And I mean that literally. The people assigning guest rooms could not see where the reservation was made. A guest who booked via an opaque third-party website (Hotwire, Priceline) had the exact same chance of getting assigned the "best" room in a category as someone who booked direct.

Essentially, each individual hotel might have their own way of doing things.