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I think what is happening is the air off the roof is coming down to meet the side air streams, when it does it sets a spin in motion by pushing on each side of each air stream, making a whirl wind, or vortex. The roofs air stream is pumping the vortexes, I am not to confidant that a lower hatch spoiler will stop them, but it will slightly change the flow as well adding the VG's upstream. If the rear hatch spoiler is made to extend to the tail lights it could deflect a lot of the top airflow off the back at that point, instead of joining the airstream further down the body.
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A hard edge under the rear bumper / extending a belly pan somewhat beyond the lower bumper line might not be a bad idea either.

Good ideas, i am going to look into that, give the air leaving the underside a purposeful flow,perhaps even filling the low pressure area behind the car.