Unfortunately Mythbusters didn't actually "prove" anything. A single experiment on the highway does not a "scientific study" make. And the "water tunnel" didn't actually prove anything except that the little vortex does form. According to what they showed on TV, it's pure speculation that the vortex has anything to do with drag. They should have tried to measure drag on the little model or run the highway test over and over and over again to eliminate all those other variables they didn't take into account.
Now, I do believe that the tailgate is better up than down, but not because I watched the show. Auto manufacturers are desperate for every little mpg they can squeeze out of their thirsty pickups and if they could get a gain out of breeze-through tailgates, I'm sure they'd do it. I mean, they spent millions on MDS. Propping the tailgate open is, well, free.