On my old K5 Blazer, I used small adaptor plates about 2"x4" that had an edge of "fake" rain gutter. I put 4 of them through bolted on the fiberglass and mounted Thule racks to carry 3 kayaks. When I removed the racks, you didn't even notice the plates, they were almost flush to the top. HTH
They used to be called "bronco brackets". Most places that sell yakima racks will sell brackets that bolt onto a shell. Most of them even include back up plates. I have been using them on my fiberglass cap for years with no issues. This includes hauling a half dozen sea kayaks (including a 22' double) at highway speeds and down through Baja. I cant imagine the stock fiberglass roof is that much weaker than my crappy lear shell. I attached a photo of the clips with no rack mounted on them. They are starting to rust after 13 years. Salty sea kayaks will do that to them.
I've used Yakima 1A mounts. You will also want the 48" crossbars. Attach the front cross bar to the truck cab raingutter and the back cross bar to the fiberglass top raingutter. Once you have the two crossbars attached with the 1A mounts, you can put a variety of things on the rack. Baskets, bikes, skis etc. They are good for about 100lbs max.
You shouldn't be too afraid to drill the fiberglass shell, Craigslist frequently has them for under $100.
My roof rails were swiped off an Isuzu Rodeo, the cross bars were shortened so it would fit between the rear windows. It's mounted with (8) 6mm stainless bolts through the shell with brake line cut to length to prevent the walls of the shell from distorting when everything was tightened down. In addition to the factory rubber gasket under the side rails I used just a touch of RTV to prevent and water leaks, so far I've had none.
Jeep Cherokee cross bars mount on the same style rail but the crossbars sit much higher (the Jeep rails are much longer but could be cut to length, the cross bars are easy to cut to width). I like this design since the weight is spread out over a greater distance on the fiberglass cap - I wouldn't want to hard mount a basket with legs directly to the roof since it would localize the weight to a few small areas. The eventual plan is to run several aluminum square tubes front to back and bolted to each cross bar to make, essentially, a roof basket without the sides or resultant mpg drop.