The two go together. In the usual case, you have a Z (or whatever) fare which has been delegated to Y on a single-class plane. When a two-class plane is swapped in, you should keep the Z (or whatever) fare and get the matching seat (and RBD on that segment -- you should be put into Z).

There's a better argument to be made in favor of getting the PQM bonus on the single-class plane than there is for not getting it on the two-class plane. (Specifically, it's because you bought the first-class fare and would have been seated in it but for the equipment). It doesn't work that way, but it's a logically cohesive argument.