This has been gone over many times on this forum, and yet there still seems to be a lot of misinformation.
First, the dealer/Ford does not need to prove that a failure was 100% caused by the tune. If the failure that occurred can be attributed to the tune, it’s not warrantable. Ford can only warranty the factory calibration; they have no idea what an aftermarket tuner went in and modified. Ford, nor any other OE, is in the business of reverse engineering and testing your modification to prove how it caused the issue.
Second, removing the tune leaves an electronic trail. Mode 9 records that information and it will be obvious that the vehicle had an aftermarket calibration installed. PCM capabilities have also advanced to the point where the PCM hardware can detect the aftermarket calibration and in some cases will set a DTC against it.
Plenty of people on this forum are running brand name tunes and issues seem to be rare. But the bottom line is that it’s important to be informed of the consequences should a failure occur.