These questions are complicated. A lot of folks will just say the Magnuson-Moss Warranty Act protects you; and Ford voiding the warranty is illegal. This is true but if Ford decides to fight you in court, I can assure you they have deeper pockets than anyone here. Technically, any part that fails that could be attributed to the aftermarket part (which BTW has to be PROVEN by Ford) would not be covered. For example, you blow a turbo (or 2) and bring the car in. Ford could say that the intercooler somehow caused the turbo failure. Again, they would legally have to prove this, but if they come back to you and say, "Hey, you're screwed your intercooler caused this", what are you really going to do?
This is close but still incorrect.
Using your example, I blow a turbo and hobble to the dealer, who thinks the aftermarket IC caused the failure.
Ford doesn't have to prove anything - they simply deny the work under warranty. There is absolutely nothing you can do to make Ford fix your vehicle for free. They will refuse to touch it.
If you think you have a case, YOU spend money getting some independent testing done, certified automotive expert witnesses, the CEO of the aftermarket part, etc some/all willing to testify on your behalf in court - which you'll be paying for out of pocket until you (hopefully) win and then get reimbursed (if you win attorney's fees).
I readily mod but am always prepared to pay if something goes wrong.