Not sure this will help you...
However, on Ford Rangers there is part of the metal bed on back left side that has an slanted or angled raised section for the fill tube to an extra gas tank that was never built for Rangers. Some guys remove the spare tire and figure out how to fabricate a mount for a Ford Bronco II second gas tank there and of course, put in a gas fill door.
This raised fill tube part prevents the botton left rear corner of the camper from sitting down all the way into the truck bed.
Not a good thing.
When I ordered the Bobcat I was offered two choices, 1) a simple cut of the offending corner of the camper with an angled piece of material put in place, which means I would have this funny shape on the inside of the camper where I wanted to put my Port-A-Potti and it wouldn't fit there if I did this option, or 2) beat down the offending part of the truck bed when it was time to mount the camper.
To fit my ATC Bobcat in my Ranger, Marty and I beat the raised metal section down with a small sledge hammer. Marty thought we were going to rip the metal of the bed or at least cause some kind of an opening to appear (he stopped working on it at that point in time and I continued on).
However, the beating just removed the paint and the thickness of the metal was good enough to hold together. I think the galvanization or base coating was still on the metal and I can see it without taking the Bobcat off. It hasn't rusted yet.
We moved the metal a maximum of at least 1.5 inches on the top & bottom of the angled raised section and a slightly larger amount near the middle of the angeled raised section, maybe 2". It was a lot of work and I'm glad I had my heavier (2 lb) and longer handled (20") mini-sledge with me. We beat the (%@& out of it.
This may work if the area is only 4" x 6", like mine was.
If you've got a bigger section, the making of a camper lift to clear the area is probably a better idea.
If you can't use aluminium and have to go with wood... seal it, coat it, and paint it well.