My roof rack weighs +/-100 pounds alone. It has 4 'feet' that support the weight and are attached to the topper with 'tracks' bolted to roof. I have hauled fuel cans, spare tires, boats, bikes, and miscellaneous stuff up there and never had the slightest strength issue with the topper or the rack. Additionally, I usually climb on top of the topper to load and tie down because the truck is too tall. In the almost four years I've been doing this there have been no stress cracks or other signs of abuse on the topper. It's a Covermaster brand.
So, I don't think you'll have too much trouble with weight as long as you have a good quality fiberglass topper. The weight of a spare tire would certainly not be a problem.
However, if you're still concerned, there are manufactures (Kargo Master?) that make racks that attach to the truck bed rails and then wrap around the outside of the topper, so no weight from the rack rests on the topper.
FWIW
Steve