I like the original design. You will always have vortices. With your design they will be lessened.
Anchoring it depends on how detailed you want to get. Ideally, building a new lightweight fiberglass/polycarbonate hatch that mounts in the factory location but is "oversized" to fit the dimensions you laid out would be best.
Ofcourse, this method is not easy
. I still think the best anchoring method will be to attach it to the hatch lid somehow. By doing so, you can make the mod reversible.
To decrease interference drag/vortices, be sure to apply large radii to all edges (if it's practical to do so...
).
I really like the look, by the way.
- LostCause