"They told me I can't even carry a bag of groceries in the bed"
This is a common misconception. The body style of a vehicle determines its classification. If you use a station wagon to haul lumber and tools as a contractor it is still a non-commercial vehicle by body style. You can haul all the rock and dirt and whatever else you want in my truck because what you carry does not matter, only that the body style has been changed to, in the words of the DMV, a "human habitable" vehicle. It is essentially like the station wagon. What you lose is the weight fee and it is not a fixed price it depends on the vehicle and how old it is. You pay the weight fee on any "commercial vehicle" regardless of the GVR. I had it listed on my Dakota before I put the shell on and it is gone now.
If you do remove the shell or camper then yes you can get a ticket for that because you have the wrong registration, hence the requirement that the shell or camper be a "permanant" installation.