I went with a heavy-duty aluminum contractor shell for just this reason. Even though I have yet to attach a RTT, I wanted the option to do so in the future without having to worry about killing the shell. Fiberglass can be successfully reinforced as suggested by other commenters, but I figured a well-built aluminim unit would be lighter, stronger, and more durable in the long run. I paid about $2,200 for my shell, and it has lift-up windows on three sides, security screening on the windows, four internal lights, insulation, and an integrated ladder rack mounted to the roof and supported by the shell's internal framing. It was expensive but I really like it. It was made to match the angles of the truck so it doesn't look like a boxy grandpa camper. An ARE fibergalss shell was about $1,500 but it didn't have some of the features I wanted, so I spent the extra dough and went with the aluminum model. So far so good.
Since I guess you already have a fiberglass unit, I'd seriously lean towards installing some sort of interior bracing to which you can bolt your rack directly. Better safe than sorry. Alternately, consider a ladder rack mounted to the bed rails and then extending around and over the shell. That way you have no weight at all on the shell. I've seen that employed a few times and I've also seen that kind of setup posted on this forum. It seems to work really well and it can look pretty good if done right.