The Warranty issue is still up for debate. My dealer does not seem to have issues with aftermarket hardware (with-in reason) and re-tunes. However, my Service Advisor advised me to bring my DiabloSport Predator with me when I bring the car in for any problems that may be engine related. Both the DSP & SCT Xcalibrator save your original Factory tune. You can reflash it before going to the dealer for service. One very good reason to return the car to OEM tune....the dealer/Ford may have updates to your OEM computer tune that is not affected by either of the tuners I mentioned. You need to talk to the resident Mustang guy in your Dealer's Service Department. He will give you the best answer for your dealer.
"It is better to ask for permission, than to beg for forgiveness"