Our 2012 Flex has a dealer installed Ford remote start system. I just bought the vehicle and just took it back for some simple service work. Part of my return was to have them disable the "door open shutdown" feature. The service dept returned with the position that it could not be reprogrammed. I found on YouTube a guy posted how to reprogram via the "program button" located under the dash of a comperable Expedition. I could not find the "program button" on our Flex. Assuming it does not have due to the MyKey option.
Here's the good news.... while hunting under the dash for my non-existant "programming button" I did locate the Ford Remote Start module. So to make a long story/project short.... I pulled the "door ajar input" wire, and "ignition key present" wire from the module and now the we can start the vehicle, unlock the doors, and enter without the engine shutting down! Just get in, insert the ignition key, turn to on position, and drive away!!!!!
Here's the hitch..... ours was a dealer installed system when vehicle was new.... I have no idea if there are similar hardware items for the factory installed versions????