yup, tailgate UP...

Read the engineers response about the "bubble". That is 100% factual. By lowering the tailgate or placing tonneau cover you are actually increasing forward drag as well as decreasing your downforce. The shape of a truck is basically a step down from the front of the vehicle. this is one of the most studied forms in fluid dynamics. this creates a low pressure zone behind the cab which in turn causes an upward and rear ward pull on the truck. the larger the step the more resitance (within limits). notice the teardrop shape has no step... hmmnnnn.
with the tailgate up you create a vortex that rotates clockwise if you were staring at the driver side door, this produces lift, but not much drag (ie less drag then bed down)...
so what you actually experience is a combination of this pocket cavitization and a step down effect. whichh effect dominates is dependant on the individual truck's design, speed, bed coverd/uncovered, tail up/down etc.
My persoanl opinion is I doubt it has ANY effect lower than 45mph, maybe minimal effect at 60ish and would start to be relevant in the 75-90 range, above that it can spell disaster (namely due to lift not to drag).
For cars like prostock trucks the lift is an overiding factor, and they have encapsulated beds. As far as drag... ITS A TRUCK!!!!! pretty much you are F'ed and you will only get minor improvements at best unless you have a full skirt from roof to tail. and that might not improve your airflow either!

I'll send you references if you want but, yeah pretty much the way it works... if you are wondering... My senior project is on Computational Fluid Dynamics.

Jay