With modern day aerodynamics, it really doesn't matter:
AS you can see the air doesn't even go into the bed. On older trucks, it's been shown (in wind tunnels) that with the tail gate up, the wind hits the tailgate, swirls up, and forms a high pressure zone that the air rides over (much like the above image, actually). I think tonneaus for MPG is a myth. Buy one because you need or want one, not for MPG!