I don't recall the Mythbusters doing covered or uncovered, but they certainly showed that gate closed is most efficient because you don't get vortices so badly.
Seeing as the "dead zone" inside the truck came in part from the gate creating a baffle that locked in a mass of still air behind the cab, then capping the bed would just kill that dead area and add a lot of weight, so it could be a lose/lose.
I'd want to see results of 3 things - gate up, no cap; gate up plus cap; gate up plus tarp.
If you regularly do the same drive every day, fill the tank to the top, run the vehicle for a week, re-fill the tank to the top and run for a week with the cap on, and re-fill the tank and run for a week with a tarp on.
After three weeks, look at how much fuel you used each week, and you'll have your answer.
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Overhead, the Albatross hangs motionless upon the air,
And deep beneath the rolling waves,
In labyrinths of Coral Caves,
The Echo of a distant time
Comes willowing across the sand;
And everthing is Green and Submarine
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