I'd buy one of these Gem Top steel tonneau covers and drill a hole right in the middle.
Agreed. I do that or like was stated earlier, pop a hole in the roof and mount you a Wilson there. Or even better, a Predator. The more centered that antenna is and above the highest point of that truck, the better it will perform. If that’s just not an option for you then get it away (however you choose) from that rollbar and/or the cab.
I’d personally suggest bonding also but I guess that’s pointless at this point unless you get your antenna mounted in an optimal position.