As Stu explained to me, the airflow over the roof doesn't come up the middle, but up and over the sides. If you look at the roof from above, then put a triangle that goes from the front corners to the back middle, the outer bits are the airflow, which then comes down over the boot glass, about two inches above it, leaving a vacuum gap where the glass is, and then comes down to conatct with the boot edge. There's a lot of turbulence right behind the boot, and the gurney flap just settles it a bit, making it more stable for cornering, without affecting the drag significantly.
In short, having one at the top of the window would likely be a detriment as it would 'spoil' the airflow insetad of reducing turbulence, which is the purpose of having one right at the back. That's why the boot lid is the shape it is, because the prototype had a sloped boot in the same profile as the glass, but the car was exceptionally unstable, so they stuck a flat bit on. It was the same story with the old Audi TT, and look at drag cars with that big flat table top hanging off the back.