Tailgate pad and tonneau cover

I don't think any tailgate pad worth a shit (i.e. has foam) will work with a tonneau cover.
My buddy somehow ended up with a Dakine pad without foam specifically only where it curls over the top of the tailgate and it sucks ass. It had to be some type of manufacturing error. He cut it open and stuffed it with pool noodle foam.

I had an Extang Tri-Fold on my Tacoma, and it worked pretty well with the Race Face Tailgate pad. There isn't a lot of foam on the top, so it fits under the Tri-Fold with no problem. The top of the tailgate on the old gen Tacoma is a bit recessed from the top of the bed though, which might not be the case with other trucks.

I used to have a Dakine, and it didn't work so well. The big foam bits on the side that are supposed to keep your bike from sliding off didn't really work. You could make it work, but not in the way it was designed to.

I have a RaceFace T2 pad on my Raptor and it works with the cheap tri-fold cover. The T2 doesn't have padding on the top, but has plenty of padding in the areas the bike touches the pad.