Don't know how this applies to the newer technology of today but as far as warranty concerning PCM tuning, back in the day, when I was running a Supra, I could interchange the ECU/PCM. One was modded and the other stock. If I were to bring it to the dealer, I would simply unplug the tuned ECU and mount the stock one. No one was the wiser.
Having a Supra forum was instrumental in what parts were affected by what modifications. We would then address the weak components and replace them with upgraded versions that would stand the stress.
Sport vehicles are generally engineered to withstand more than stock power but there's always a breaking point. Keeping in touch with other owners, let us know those breaking points and the remedies for them. When you play, you pay!
It also helps to have extended warranties by companies that let you use any certified repair shop. So far, my experience with Ford corporate confirms that there are many other mechanics that I'd rather deal with.
Thanks to all that contribute invaluable info on this site!