Ok on this image I was wondering if maybe a more contoured fit around back of tub might work better?
You could make a like shape that bolts and glues Sikiflex is one of my fav adhesives to the top portion of cab and shape the rear hatch accordingly and it could seal over the outter portion of rear tub....hope I am articulating what I mean?
It woukd be easy to skive some additional panels to the sides and obtain shape as required I suspect.
Just thinking outloud...
Nice work regardless