Okay, here is what we learned: Starting in 2009, CARB/EPA required that the Viper skip shift diagnostic not only performed a simple circuit check (as it had in previous years), but also include a rationality check to determine if the skip shift actually took place. This means that you could no longer install a simple load device that looks like the solenoid electrically such as used in previous generations. Simply said, the rationality check looks for the correct rpm drop when the skip shift is enabled and the vehicle shift occurs in that window and if, after six consecutive samples the rpm drop is not correct, it will throw a CEL as it interprets it as a malfunctioning system. The Mopar controller eliminates that of course.
Going back to your Georgia emissions, we have a customer in Atlanta who uses the Mopar controller with various other mods. We believe that he simply swaps out his original controller as needed, making sure to get in a few drive cycles beforehand so that the system relearns for any potential testing. We haven't heard of any issues.