You've got a mix of aluminum and wood:
https://www.allterraincampers.com/uploads/framefull1280x960.JPG
The ends are the problem. You could probably carve on the base, but then it likely wouldn't fit in the truck because of the sidewalls of the bed. It would require a new door, welding the frame together at the new height both front and back, and being sure the fender wells clear properly. You would also be lowering the cab to overhang clearance. Frankly, it might well be easier to build one that satisfies the HOA than to modify an FWC or other aluminum framed camper. I also assume the HOA does not want your truck in the driveway so using the garage to store the camper while the truck sits out is not good (the dolly solution) and the garage is not large enough to accommodate the camper and the truck when separated.
As an aside, I wonder if you could even build a cabover that was usable that would fit into the garage opening. You might look at older Alaskans that are non-cabover models to see if they were significantly lower. My memory of my Alaskan (years ago) was that it sat about 4 - 5 inches above the cab of the truck. Heavy, yes. Your truck might not carry one for the weight/dimensions.