I actually have a 2012 Ford Focus with MyKey and Intelligent Access. (Single button push start)
In the manual it states "as an added security feature, the engine will shut down when any door/liftgate/hood is opened". I looked but I could not find the program override button, so I took it to the dealer with the printed out instructions you posted. I had them working on it for a few hours, which the called the 3rd party vendor to find out option 7 is no longer available, and the engine shutdown is a security/safety feature. The dealer told me the vendor said there is no way to disable the door sense feature.
The remote start system is PowerCode which is AKA Audiovox. http://audiovoxproducts.com/codealarm/ aka codesystems.com.
I think I wasted $450 on this system. I will call Ford and complain, but its useless to me if its just going to shut the car off.
Thanks again
Mike