The shop would have to prove your headers caused another part to fail in order to not process the warranty. That may seem difficult but it's really not.
I had a friend of mine put a CAI on a Honda Civic SI. One of the new ones. About a month later he blew the motor. Took it to the service center for repairs since it was still under warranty. The dealership denied the warranty stating that the CAI made the engine run lean which is what caused the motor to let go. He had to escalate it all the way to Honda Corp. to get it taken care of. By the time that was done, and he had his car back, he had been without his car for 3 months.
Yes that is a rare case. My advice would be go talk to the service MANAGER at the dealership about how they handle modded vehicles. Don't just talk to a tech b/c what they believe is policy is often times very different from what the actual policy is. If the service manager is a dick, take it to a different dealership if their is one close by and see what they say. Then make your decision on how you want to go about modding the car.
i say put the headers in and if you ever have to get it serviced at the dealer under warranty or your engine suddenly goes just make sure you have the stock ones as well and have someone you know replace them for you or DIY I doubt the dealer would figure it out. then when you get ur car back put them back in. there may be some unnecessary hassle but i think its worth it and i was actually thinking about doing the same thing lol
same here had a neon srt4 because of the modified exhaust the voided my warranty when the stock engine spun a rod bearing, later found out it was undersized bearings from factory just make sure its stock if anything happens to your engine etc. taking it in for oil changed and such wont throw a flag for the exhaust so do it and keep ur stock ones.
On my 2004 GT I put in a set of Steeda under drive pulleys. About a week later my CEL came on, and I pulled the code (P0340) - camshaft position sensor. I took it in and it was somehow related to the alternator (aparently this is a common issue). They put in a new alternator for me even though there was clearly a different intake, throttlebody and set of pulleys on the car, in addition to being lowered & having a Cobra R front bumper.
If you have the capability of doing the install yourself, just do it. In the slim chance that something catastrophic happens to the car/engine, you can swap the stock ones back yourself, though it would be a pain to do so.