The Magnuson-Moss warranty act does cover this very thing and can protect you. However, if the problem you are having has an aftermarket mod done to the same, they can make your warranty claim go 'poof'. Although they must "prove", even then, that the specific mod caused the problem, it is easy to deny a claim. And imagine how easily a judge, who probably knows nothing of mechanics or electronics, could be convinced in small claims court that your 'related' mod caused the problem.
Bottom line, if something does happen, don't just let them tell you "yep, that caused it". Make them prove it. If they came to this diagnosis by using test equipment, service manuals, or visual methods, it will be easy to reproduce that same diagnosis for you. You will find that 99% of the time they have just guessed that this caused the problem and did no such research. This will become obvious when you ask them them to show you in detail how the diagnosis was achieved and they refuse or become agitated/angry.
I have considerable experiences in this last scenario from when I used to manage custom car audio shops. When something went wrong with a new car the dealership would see aftermarket audio equipment in the car and just assume that it was the fault of it or the installer. Trust me this challenge to them works. It will either get them to fix it, show you that your mod did cause the problem, or that they were full of poop and they are pissed you found out.
One example before I shut up. A custom system put into a new Cadillac. Next day the check engine light comes on and the customer takes it to the dealership. After 3 hours the dealer says that the new sound system is to blame. She comes back to us and I check my installers work personally. Nothing wrong. I get in her car with her and drive back to the dealership to talk to the service manager. We agree that the technician will come out and talk to us, and that's when i hit him, not literally.
I patiently let him explain that the car audio system is to blame and that it will cost over $1000 to put in a new computer. I then ask him a very simple Q. "Show me how you came to this diagnosis, and where specifically the problem lies in our installation". He tried to dodge it with turbo-spew. I again restated my Q and he refused to answer. Service manager now back with us and the mechanic admits that he did no such troubleshooting and just assumed that the aftermarket mod was to blame. Turns out it was a defective 'catastrophic' converter that had triggered the service light, and not our system.
Cold busted and he's apologizing to all involved. I have done this numerous times and had similar outcomes. Just make sure you are not at fault before assaulting the dealership. Also don't be fooled that this is just a service technician problem and it is not done at the behest of the service manager to save time and make money. I am not saying that all, or even most dealerships or technicians are bad. But you will know one when you find it and now you will have an easy tool to figure it out!