Could it be that the shape of the front cap on your 5er is directing a lot of wind down into the bed ? I have carried a multitude of things in my P/U bed, both in front of and behind the hitch, and not much of anything moves.
As for the cover you are thinking about making, if all your pivoting, both front-to-back and side-to-side, is above the bed rails, then I don't see why your idea wouldn't work. The only other thing that might decrease the turbulence would be a replacement tailgate that lets air through, like some of the bar or lattice types.
2003 Ford F-350 V-10 Crew Cab 4WD Long Bed
2004 Jayco Designer Medallion 29 RLTS 5th wheel
Bill, Gayle, and Mindi (dachshund)
Retired at last !
Nothing is foolproof to a sufficiently talented fool.