These are theoretical ratios in perfectly dimensioned rooms. Real rooms are not always rectangular, nor are the walls perfect reflectors. Dr. Toole covers this in detail showing acoustic center of your rooms are different than computed ones based on dimensions. Regardless, even with the recommended positioning, you need to measure and apply EQ. As I noted, you can only fix some modes with subs on top of your mains assuming you pulled them out of the room that far.
As to concept of "plane wave" as you described, that just means that the subs are close enough to be treated as one. If they are, then they are not doing any mode cancellation.