Not at all.
Here’s an ‘official’ response from FP:
The FPP 3/36 covers failures *directly* attributed to our parts, for 3/36 from the in-service date of the vehicle. Outside of that period, the factory warranty still applies, however *if* there is a failure that is directly attributed to our parts, then that specific claim could be denied. For example, if you had a water pump seal start leaking, obviously that wasn’t caused by our parts so it would be covered. If there was something along the lines of, say, a piston burned up from going too lean and it was determined that our calibration didn’t provide enough fuel, then the base warranty likely wouldn’t cover it. It’s a case by case basis.