Speakers on top of subwoofer

This is not a problem. Simply use a vibration isolation pad/feet between the speakers and the subwoofer. 

Think for a minute how many expensive large floor standing speakers have large, vibrating bass drivers in them. Too many to count AND they have no way to eliminate bass energy going throughout the speaker and crossover since they are connected to the same cabinet as one unit.

One other big advantage is the subs would be positioned properly for stereo image especially if using higher crossover levels. ( Subs set with slightly higher crossover can be locally identified)

You also gain an advantage to isolate the two cabinets in your set up  and still properly aligned. Highly recommended.

@ghdprentice    Don't do this? Wilson is doing it wrong?  BTW...these go down to 20 HZ.   B&W, TAD and many others do the same split configuration.

@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.

@soix 

vibrations negatively affect sound, so adding significantly more vibrations into the speaker is just never a good idea, period.

Agreed, but that's NOT what I'm suggesting. I want to eliminate all vibration going to the speaker and it's absolutely possible. I agree that the tweeter height must be within range of your ear height. If it's too low the speaker can be adjusted higher using stands. The only problem would be if they are too high. You are assuming this mismatched condition is "Likely" when it hasn't been measured and we don't know.

@mijostyn   

Isolation feet are for the most part a joke. 

Believe it or not there is big difference in the dampening affect from different materials used in vibration control. It's not a joke, it's science.

@lewl28  Too low can easily be raised higher by the simple use of some speaker stands. I cut mine to an exact height.

What crossover do you set you subs? 

A thought to ponder... when I move subwoofers around a room I could always, easily detect where the sound was coming from. I could always point at their location. The higher the crossover the easier it was to hear their location. If used in a stereo application this can affect the stereo image negatively. By placing the Harbeths in straight vertical alignment with the woofers will retain the stereo image and depth. They will still be adjustable. Initial placement YOU control, change the phase, change crossover level, change the volume, toe them in or out.. Plenty of adjustments. For me the center image was more important than attempting to find the last ounce of bass and separating the subs and have two speakers off the center image. 

Many others feel this way also.