Magnuson-Moss does not apply to replacement parts that are not OEM-spec. No matter how many times sellers of aftermarket performance parts say that it does.
It's intent and purpose is to allow independent production and sales of aftermarket replacement service parts that are OEM-spec, namely oil filters, windshield wipers, brake pads and rotors etc.
If an aftermarket oil filter that complies with OEM specifications causes your engine to blow - only then the manufacturer has to prove something before denying a claim. If your non-OEM intake causes detonation and kaboom, the dealer doesn't have to prove a thing beyond the fact that the intake is not up to OEM specs.
Where it gets murky - when the modification makes some well-known OEM flaw show up sooner. In that case you're morel likely to succeed in pushing the manufacturer to eat the repair no matter what mods you had.
Here's a read on the subject from the other side.