Apparently you've rather fixated on the layer of air within a few inches of the car, while not totally insignificant, it is really pretty insignificant compared to the huge volume of air that is being affected by our vehicles as we plow through it.
Keep in mind that ideally, our cars are moving through through calm air....the air is not blowing on our cars. When not ideal we are moving along in 6 lanes of traffic with a 25 MPH crosswind....program that into your CFD calculator.
The ultimate goal of aerodynamic drag reduction is to move through the air and displace the least amount of energy into moving the air out of your way, and falling back to calm again after you've passed, as quickly as possible. The less energy expended on making air move about, the more energy you save.
When you consider the amount of energy it takes for a fan to run and blow a little breeze around your room, then relate this to a car that is dragging a fat column of air behind it for a few hundred yards and moving air out to 15 feet in front of and around the car, you realize we a driving in huge fan blades that are stirring up the air. The most efficient shapes allow the air to move back into place in the easiest way possible while not creating any trailing vortices.
The layer of air next to the car has a small impact on the big picture, but the overall shape of the car is really what matters. You can't wrap a pig in a mink and call it a mink. For the ultimate drag reduction, build a VW XL-1.
You want to reduce the drag of a pig? Good luck with trying to mess with less than 1% of the air that is being displaced by the car and hoping the other 99% will bend to your will.
In so many words Aerohead is trying to tell you computers still really suck at trying to figure out aerodynamics because a car is constantly affecting 140,000 cubic feet of air weighing 12,000 lbs as it drives down the road and it's really hard to say how this air will behave. Not to mention it's all numbers in and numbers out on the computer, the numbers in thing is very subjective and a few missed assumptions on the input can create large variations from reality on the output. GIGO. I don't even pretend to know a lot about it, I again just listen to experts that say these things.
By saying you're going to dimple a car, you are asking the 6 lbs of air at the surface of the car to change the behavior of 12,000 lbs of air. (That's not really 1% is it?)
Here's the Hot Rod magazine article I alluded too. Scroll down to the "Aero Stuff That Doesn't Really Matter" for the Golf-ball thing.
Car Aerodynamics - A2 Wind Tunnel - Wind Camp Tech Theory
Anyway, fun stuff all of it! Keep learning!