Coming from the car that i came from recently, i know all about the world of getting your car warranted and not getting it flagged for modifications...

The Magnuson-Moss Warranty Act
http://www.dynosources.com/dept.asp?d_id=203&l1=203

It basically says that a dealership can not refuse warrenty work on a car solely based on the fact that a car has aftermarket parts on it. The dealership has to prove that the modification added to the car was the direct cause of the failure to a stock part for them to void your warrenty.

Of course, if the world worked the way it should, that would be the end of it. In the real world, lets say that you blow your tranny some how, most dealership will refuse the warrenty work and void the warrenty for something like a throttle body, or even a Intake. I have a friend right now that has a SRT-4 that had his voided because he had a intake while he was in for a tranny that wouldn't shift into 3rd gear.

The real world stance of the dealership is that you have to prove to them that your aftermarket part, regardless of what it is was NOT the cause of the failure. Most people play the game of returning the car back to stock when they have to bring it in for work at dealerships.

Now, dealerships have seen it all... so they tend to be skeptical... too many people try every which way, and they mess up something on their car after they did something.

Last thing you can do is be honest with the dealership. I had in the past, while i had a srt-4 with coilovers, sways, intake, stage 1 pcm and a couple of other bolt-on parts, the cam seals blew, i went into the dealership and told them what i had done with the car, and the problem. If they could look at it and fix it, if there was a problem, let me know before they do anything.

So, basically if you want to play the modding game, be ready to have to pony up the money when something goes wrong. It isn't always fair, but it is just the way things actually are.