The last 2 times I went to the dealer, I was given no hassle about warranty work for any of my mods. I have since installed my SSQV, but my dealer knew that I had a ongoing boost leak and that I was going to change it.
Striker- You should inquire to your dealer about their reasoning in this matter. The original setup used hardpipes, and I can't see any reason why a larger IC or a set of hardpipes would void the powertrain warranty.
BlkZoomZoom- What sort of problems may arise from making the car breathe better with a larger exhaust, and providing colder air for the engine via larger IC+CAI??? I don't see what a dealership could prove in court to justify voiding the entire warranty. I mean, say I had a problem with the turbo not getting oil, for whatever reason. You're telling me, that your service manager would claim that one of my mods caused this, without a doubt???