D and S continue to work as they do stock. S will continue to have more pedal multiplication for throttle, lock out 6th gear, and allow access to manual shifting. No change from stock.
There is NO need for an extra PCM in this application. In some vehicles (modern dodge, jeep, chrysler, ram) and some older cars, it is/was required to send your PCM off to be unlocked prior to reflashing. With our cars, the tuner itself is capable of unlocking the PCM and performing the reflash.
Even if Ford has some way to tell how many times the PCM has been flashed, they have no way to know if it was flashed with an aftermarket tune. For all they know, it was flashed with a stock tune a 100 times trying to get the PCM to accept the tune. My car has been flashed at least twice by the dealer alone.