Interesting thread. I agree with others, there is way to be guaranteed your modifications will be covered 100% by the dealer (or manufacturer). My experience in the auto industry has led me to believe this more because the dealers of higher end cars (i.e. BMWs) want to offer said upgraded parts themselves along with the manufactures who make approved products for various manufacturers (not just BMW).
Obviously the automobile manufacturer wants to keep people from tearing up their cars and then claiming a warranty repair, but they also stand to make a few bucks by pushing their own performance parts. I'm sure if you had engine failure and there was a K&N intake on there could deny it where as the same engine with a BMW Performance intake would be repaired (regardless of who did the installation).
Ultimately it comes down the dealer. In my experience most repairs were left up to the Service Manager to decide if they were worth fixing under warranty. Often we repaired things that weren't covered because we wanted the repeat business. So if we had someone that trashed their vehicle but brought it to us for all of their paying service (oil changes, tires, brakes, etc...) we would fix it and look the other way and claim it as a warranty repair.
The auto industry is very corrupt when it comes to the dealer side.
2011 BMW 328i by weekend, various airplanes by week.