@soix What exactly is the "design change' allowing the Wilsons to have the speaker on top of the sub cabinet?
Maybe as @steakster points out... Wilson uses The new V-Material, which is used where two parts of the cabinet come together, "behaves like a vibration absorber," according to Wilson.
You can add a world class 'vibration absorber' on the Harbeth/subwoofer also! Vibration absorption is not exclusive to just Wilson audio. Easily measured also.
'the best place to put subs for optimal bass in a room is pretty much never where the speakers are placed'
Then, according to this statement, you can conclude that the Wilsons can "never" be correct. Since the speakers are always connected to the subs and according to you, they shouldn't be.