Here's a Ford document you might find helpful. It gives dealers guidance in how to deny warranty claims when failures are caused by performance modifications.
It has the following language concerning the ignition counter referred to in the post above-
Section B: Determining the Existence of an Aftermarket Calibration
This section should be used when the vehicle being serviced currently has or possibly had an aftermarket PCM calibration.
Compare ignition counter (IGNCNTR) value to vehicle service history. If counter value is abnormally low and there is no history of a recent reflash, investigate for an unauthorized reflash and signs of aftermarket tuner connections...
Low ignition counters in conjunction with any of the failure modes, symptoms, or indicators in Sections A or C suggest possible aftermarket modifications to the vehicle