I drilled a couple holes in the sole of my Supershell to verify the thickness. It is indeed 1/4". I considered the @twhisper solution, but that would be more work peeling off and replacing grip tape and getting a new flat pad. It would also require a bigger toe rubber to get my foot in to the same position. I measured the pad on my D3 trick RTP (assuming it's the same material) and it is a little less than 1/4" and although it is firm, it is still a bit compressible. One of the reasons for replacing the foam with grip tape was to have a firmer connection to the ski.
I cut out a couple pads for under the plate from 1/8" rubber I had laying around. The rubber is flexible so as not to affect flex but not significantly compressible. Standing on the floor with my boot on and bare rear foot in position, I can feel that without the 1/4" added in the back shoulders come forward to balance and hips go back. With the pads under the rear foot I don't have to try as hard to straighten my back leg or bend my front knee to balance.
Leveling the binding has certainly been talked about before, but I always thought "close enough". @Fam-man Thanks for bringing this up. I'm kind of excited about trying this out, I think it's going to make a difference for me. Course goes in Thursday.