As Wikipedia summarizes:
"In the US, the Magnuson-Moss Warranty Act prevents manufacturers from voiding warranties solely due to tampering. A warranty may be dishonored only if the tampering actually affected the part that has failed, and could have caused the failure."
I have already demonstrated how an incorrectly paired TouchID sensor compromises the Secure Enclave, and how a compromised Secure Enclave compromises the entire phone, regardless of whether TouchID is enabled or not. Therefore, as the summary states, Apple has 100% legal grounds to state that the part caused hardware failure, being that the Secure Enclave is physically on the Apple A series coprocessor, which is a physical part of the phone. The only chance Apple has of losing this battle should it go to the courts is a lack of technological understanding by the judge or jury.
First, just because the system works as designed doesn't make it legal. It is precisely their design that is anti-consumer. Second, if the secure enclave is not physically on the sensor itself, as you say, then it seems this pairing issue can be avoided by a better design.