Dave
If you bypass the controller, you've taken it out of the electrical "loop" and it makes no difference what the dial is set on, it's now a non functioning decoration. The purpose of an autotune is to set the Auber to your particular smoker. You do a multi step autotune program to try and cover all situations. If you look at the post about autotune results, you'll see readings all over the place. I don't have an explanation for this, other than it's not a scientific experiment. I personally think I know what the Auber settings should be for Smokin It smokers, but that's just my opinion. Once the Auber is autotuned for your particular smoker, you're good to go on any way you want to use it.