Jason, I am too lazy to go look at the code, but, I think the factory chip was programmed to turn the fan on around 200 degs. In many cases, this meant that the fan did not run when the car was going down the road at speed because the system was adequate to keep the car below the turn on temperature when moving rapidly.
Now, when we reprogram the fan to come on at 168 degs, or whatever number the programmer chooses, the system, in the summer, cannot cool the car down to this number so it runs all the time. The fan then becomes a resistance to air flow as you suspect. It may speed up some, but I would bet that it still blocks air flow somewhat.
And, whatever the case may be, the AC trumps all because it is a mechanical switch programmed to make the circuit when the pressure reaches a certain level.