With the stall mat, the TC clears ok. But, on bumpy roads the cabover looks like it gets close. There are some black marks around the shark fin on the fiberglass, so I think it's barely making contact but not enough to hear or cause damage. NL suggested a different mat because they consider stall mats too hard and recommend a 3/8" rubber mat like a dee zee. They also agreed that adding support beyond the bed wouldn't hurt but didn't go so far as to say it would help.
I read about GM beds being crowned and thought stall mats could create a similar situation by bowing down at the last rib. Since they don't provide much grip against the fiberglass bottom either, they seem like a poor choice all around for my setup.
I think I need around 1/2" extra height (3/4 -> 1-3/8), a bit more length at back (thinking 6-8" overhang), a block at the front (2x8 to match bumper height when loading), and a better rubber mat (1/4 to 3/8 softer rubber mat). I am leaning towards full plywood covering the bed just to help keep it aligned (CDX unless I find a deal on PT). If so, I'm thinking 2 layers of 1/2" glued with sub-floor cement and jig-saw so th seam isn't lined up.