The way I understand the MMWA, and as explained to me by two different dealers and a family lawyer, Yes, Ford has to show the burden of proof that a given modification has damaged the engine. HOWEVER, Ford can, and obviously will, void and stop your warranty/warranty work if they make that determination. Now, for the customer to find out how Ford went about determining the cause of the failure as being related to an after market part/tune, you have to call their bluff. In other words, you have to put up some money to see the results. You have to get a lawyer, go into mediation and at that point, Ford will take the time to explain it to you through their engineer and their lawyers. If you and the arbitrator disagree with Ford's findings, it's off to court you go.
Someone correct me if I am wrong. Where you hear stories of people simply mentioning the MMWA and getting their cars fixed is when a dealer is saying that since you put on a different oil filter, you voided you engine warranty and that different filter is what caused your engine to blow up. Or, you have a head gasket blow and it fries a head. But since you had headers installed, they try to blame the failure on the headers.
If you go installing a tune, you're taking a potentially expensive chance. 99.5% of the folks out there will never have an issue with using after market tunes from a reputable place. It's those folks who use tunes from a local tuner who knows very little about the new Coyote PCM that are REALLY risking it all. That's why I went with a tune from a mass marketer of tunes like AM or BBR. They have the volume of cars and the interest of their own business success to ensure they have plenty of experience with their tunes. And they have the cars they write tunes for for the most part.
Gotta use some common sense in this folks. The MMWA doesn't provide protection, and was never meant to provide protection, for car enthusiasts who change so many variables about how their engine performs. It was meant to protect people from getting FORCED into buying OEM parts for their cars. As long as after market parts meet or exceed OEM specs, then they won't have an issue being used. This doesn't apply to tunes.