The example in the MMFF article is logical and based on common sense: A CAI has no bearing on the failure of the A/C system. Unfortunately, most CAI's require a custom tune to use a different air transfer function. And coincidentally, there's a parameter in the engine calibration that can set the A/C to shut down depending on throttle position (WOT cut-off). Now, a dealer could argue that the PCM was reflashed by an unauthorized/non-factory person using a non-factory calibration with the WOT cut-off set at an extremely high TP causing the A/C to blow up when the driver of the GT went WOT. It's a longshot, but it's feasible.
Damage caused by modifying the MAF (swapping out the stock MAF) can result in transmission failure, cat failure, engine failure, etc... because it is a vital component in your car.
That article is a good primer for anything bad that might happen in the future, but they are missing a key component in most aftermarket modifications: the tuner that flashes your PCM with a non-factory calibration which essentially modifies several core systems of the car nullifying many common arguments to defend the owner of the vehicle.
Digression warning:
Depending on your state laws, your results will also vary because state laws generally over-rule Federal law. Case in point: Under Federal law, you can own a 16" barreled AR15 with a threaded muzzle and use detachable 30-rd STANAG M16/AR15 magazines along with a collapsible stock. Under NJ, CA, and NY law, there are limitations on the muzzle (can't have a flash suppressor), stock, magazine capacity, etc... Federal law also allows you to own machine guns (M60, M249) and SBRs (10" barreled semi-automatic PS90) but that's not the case in certain states due to state laws. I doubt there are any state laws that take away your rights when it comes to warranty-related car repair, but the comment about federal law applying everywhere caught my attention.