Notice that in the Ford Fusion picture, the rear deck element is raised up a significant amount in relation to the initial vertical placement of the trunk. If visibility is not a big deal in your car, then you could make your rear deck element about 3-5 inches above your trunk to get a much smaller transition area, which could greatly reduce that turbulent bubble behind your back window.
I wouldn't try vortex generators unless I had a degree in Mechanical/Aerospace engineering.