Being a commercial pilot, I think my two cents has a reasonable value on this topic.

There are lots of different types of drag. Some of these include induced drag, form drag, parasite drag and profile drag. Ignoring all forms of drag caused by the shape of the body of the vehicle (some curved surfaces could produce lift, thus causing induced drag), a tailgate in the verticle position acts like a great bloody speed brake on the fuselage or wing of an aircraft. Whether the vehicle engineers design the cab to minimize tailgate drag in this configuration... I don't know? But... a flat board that is perpendicular to the relative airflow of the vehicle will create a good amount of parasite drag. For further information read the book "Aerodynamics for Naval Aviators". There are equations and text to describe all of this.

On some aircraft wing designs, vortex generators are installed on the top of the wings in order to delay boundary layer seperation of the airfoil. The small vortex generators actually create a small amount of induced and parasite drag. The funny thing about drag is that some types of drag (induced) decrease with speed, while parasite drag increases dramatically with speed. On a velocity vs. drag graph for a specific airfoil, the sweet spot is where the two intersect...

Getting off topic but... I don't think there is too much of a difference. The cab probably shields the tailgate's effect on drag. An interesting airflow probably does occur in the truck's bed that could cause the tailgate up scenario being the best or non the worst. If the tailgate was higher than the cab, definitely. It just depends on the truck's profile.

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