ok i've looked into this and talking to our electrical guy at the dealership i work at, (he's already told me to get a bigger turbo, and has given me more bad ideas lol!) and depending on the warrenty concern ford will ask for the tech to send them module data using the ford IDS, and if its tuned they will see the dates which it was recalibrated, and if its a ford calibration. so everytime you switch tunes the pcm saves that data, even when you revert to stock all the footprints are there. we can find this info out too with the IDS, but most tech's dont know how to, or dont care to look this up because of flat rate pay.
the good news there is a way around this! first you need a car with a virgin pcm that has never had a tune or a factory re-calibration, and then using the ford ids you can get the AS BUILT DATA and save it to a flash drive, then you can tune it to your hearts content, and if you ever need heavy warrenty work where you might be worried about someone finding out about a tune, just load the as built data to the pcm from the flashdrive and everything is reset in the pcm to the way it was upon first start up with NO footprints. the downside is you need the ford IDS to accomplish this, or an accomplice at a dealership. lol i still havent had time to save my as built data yet, but if you have an IDS i could steer you in the right direction, but dont have any step by step instructions yet.