I have the stock GMC rubber bed mat. It's about 3/4" thick and I think it absorbs some road (could be my imagination ;-
. Andersen said no problem.
With this post, let me add that I also use a Curt 4" ball extension. The Curt replaces the flip-over ball with one that is mounted to a steel plate and basically moves the ball 4" back toward the tailgate. I wanted more cab clearance but did not want a slider. Why this note is important is because the Curt also raises the ball position.
If you look at the Andersen videos etc., you will note there are two pins in the setup. The top pin holds the ball into the top of the pyramid. The lower pin locks the frame onto your bed ball. Each pin has a cotter latch that keeps the pin from sliding out. Nothing special here, that's the way all pins of this type work.
If you do as I did and choose a Curt extension, then you'll find that the thickness of the Curt means the holes for the lower pin now line up inside the center pyramid tube, basically, you can't slide that std. lower pin in (it's too long). Andersen has a brilliant fix for this. They will send you a shorter pin. You place the tube over the ball, insert the pin, then lower the pyramid down onto the tube. The entire pin holes slide up into the center tube and the cotter clip is no longer needed. You then tighten your top 2 bolts and 1 front bolt and you're good to go.
So....if you plan to use a Curt 4" ball extension, be sure to tell Andersen so they can send you the clip-less pin. It's free. It's easy. It secures the pyramid the same.