Here's my guess on what is going on which builds upon what is already suggested: With the bed fully covered, the turbulent air immediately behind the cab effectively rolls opposite the direction of travel. The lower part of that vortex tends to be slowed by contact with the bed cover, creating successive smaller vortecies the further back you go until the airflow reattaches near the rear. With the front part of the cover removed, the vortex created immediately behind the cab is much larger, but because of the cutoff at the leading edge of the bed cover, it does not propagate past the cutoff - effectively providing a single large vortex that requires less energy to sustain. (More like a big ball that just rolls in place behind the cab.) Without seeing test results, I would bet that the ideal length of open bed closely matches the total depth from the top of the cab to the bed floor.
In essence, this rolling ball of air provides a Bernouli effect to more smoothly route the outer air back down to the bed cover.
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