Depending on how it attaches to the bedrail, could you have a bracket that mount to inside of the bedrail, comes across the top flush, then rises and 90s over for an antenna mount. The antenna and coax would be sticking out past the edge of the bed, though. But access to the bed wouldn't be restricted when folding back the bed cover. Just a thought.
I'd be out with the drill and mounting it on the cab roof if I had one of those. Any reason not to?
Must admit the fender/hood solution isn't my favourite either. OK if you're in the outback in Oz or on the African plains and doing proper offroading but for driving down the highway it just looks daft.