Harper, Just a thought, but maybe it could work.

Section a few peices of plywood the same thickness as the base of your sunpad, cut them to a rectangle large enough to cover the area around the base of the scoop.
attach these from the top of the hatch directly to it.
Measure, and cut the same size rectangle from the base of the sunpad, leaving the foam and vinyl.
Cut out just enough vinyl and foam to get the whole pad to slip over the scoops (this stuff will stretch a little).leave enough vinyl to pull it through and attach under the scoop. ( if flush mounting the scoop, may need to attach "tighten vinyl" by using fasteners through the "throat" of the scoop)
This would allow you to trim away only the foam you need to, and keep it tight to the scoop.
Pretty tedious, but it will give you the look your going for, the only difficult part I see is getting the material tight enough at the scoop, might need to release the vinyl from the outer edges of the hatch to loosen it, and then re-stretch and attach after the scoops have been done.

Good Luck, and if you see any flaws in my plan, please let me know, I'll try to help you work through them.