I haven't made up my mind what I'm doing just yet; but I'm tempted to have a bracket made for mine. I don't have the bed rail system, but I plan to have either a bed cap or a tonneau cover installed before winter. I'm not sure I'm in the mood to punch a hole in the roof just yet...
So, I'm thinking of getting a piece of stainless, about 14" x 14", give or take. Long enough to span the distance between two of the bolts of the bed rail system, which are about 13" apart. The flat portion would be about 6" long, to get the antenna mount past the bed rail. Then a 90 degree bend, then two more 90's, so that the remaining lip can be secured to the bed rail system mounting holes.
In my case, I'm thinking of two antennas, one for 2m and the other for 11m, hence the 14" length. If one wanted a heavy antenna, the long length is ideal. Alternatively, for just one antenna, I'm thinking of using 1" square stock, like aluminum, 14" long to span the bed rail system. Then on that use a thinner L bracket, say again 6" long to get the antenna past the bed rail, then just one 90 degree bend and then attach to the square stock. [From what I've read, the bed rail system uses 6mm bolts, with a 1mm pitch.]
Haven't gotten anywhere on the idea just yet, but it's what's kicking around in my head at this time. This would allow usage of either kind of bed cover, and leaves the Bullring tiedowns that are already in the stake pockets. And not require any cutting/drilling/other mods to the truck.