It's difficult to give confident advice without knowing the construction of the cap. Since you said it was made by the Amish, we can't even guess. Is it wood? Fiberglass? Injection molded?
In general, I would avoid penetrating through the cap, because of the likelyhood that it will eventually leak. If the roof is thick enough, like 1" or more, I would screw into, but not through, with wood screws. That should work with either wood or fiberglass.
If it is wood, epoxy can work very well, but you will need to sand through any finish before you apply the glue. Consider just gluing square blocks about 3" square of 3/4" high quality plywood like Baltic Birch. Then screw your rack to those blocks.
Another way to skin this cat would be to drill through the sides of the cap, into runners along each side, and then build your rack off those runners. If you must penetrate the cap, you will be better off doing it from the side so water will run away. Use some silicone and stainless steel fasteners. I would reserve this idea for fiberglass caps only. Wood swells and shrinks too much, and the penetrations will leak no matter what you do.
Check out a fastener call a Jack Nut. They work similar to a pop rivot or one of those dry wall anchors that spreed apart when you tighten the screw. They come in many different thread sizes. Fortunitly my work has a gun type tool to make them WAY eaiser to intall but I dont know where they got it. I'v mounted 20 rods and reels to my cap for a Canada trip I normally only have room for 10 but I added an extra rack for the trip. I've also mounted lights and eye bolts to hang stuff from. The last place I got them was Sears hardware. Your cap should have a double wall somewhere you just need to drill on the inside and there should be enough gap to get the Jack Nut in and get it pulled tight. Once its in you have a nut up in your roof now that you can attach any thing to. I passed the Jack Nut thru a fender washer first to give it more support and so it wouldnt bottom out in the hole. There is a similar thing made of rubber but they rot out over time. If I could send a picture I would but I cant figure out how to do it this is my first time on this site.