It seems pretty obvious to me that the air flow dynamic was in a more concentrated ie" more aerodynamic" flow form when the gate was up. If you look, there is much more diffusion or turbulence with the gate down, when it was up, the air stream was concentrated and more even, and flowed right past the gate, no turbulence whatsoever. It's very clear, to me at least, that there would actually be more drag with the gate down... Just look at the air flow with the gate down, it drops down and hits the bed and begins to diffuse, creating turbulence, ie drag..
Someone made a good point about safety, and the tailgate securing the bed, this is very true, I don't have science to back up my claim, however, I drove with the gate off for a month and notice the bed flexed allot, you could actually see the rectangular hole where the gate should've been, go from rectangular shaped to more of a parallelogram when cornering, there is allot of rigidity added to the bed when the gate is in place for sure...