You're mistaken about the conventional wisdom, and you're mis-reading the website. There are indeed two lists, but they have the same order, except that the tie-breaker for CPU's changes from time of booking to time of check-in. It would be kinda insane if someone waitlisted with an instrument didn't get priority, IMO.

Incidentally, I do not believe that uncleared Y/B/M's are considered displaced F passengers. Although displaced F passengers are yet another category, which is at the tippy-top of the list.