I run a companion. First truck had a sprayed in liner. Worked fine with the hitch. Present truck has a rubber mat. B&W's present day instructions says to cut the mat under where the hitch rests on the bed - two huge rectangles. I didn't cut the mat and it does squash down under the weight.
The original instructions for my hitch said it could sit on top of a drop-in liner. I wouldn't have done it then, nor would I now. Too much weight/stress being put onto a piece of plastic.
If I were in your shoes... a couple options. Sell the liner and get what you can towards spring in or mat. OR you could cut out the entire bottom of the liner and put a mat down on the bed of the truck.
Up to you, but I would not trust the weights involved sitting upon a piece of corrugated plastic.