Dealers will almost always give you a hard time when dealing with aftermarket parts replacement. I used to work for Chrysler and the things they would say to make customers pay out of pocket when it should have been warranty was incredible. Yet some aftermarket parts you can get from the dealer parts counter and have installed without an issue. Bottom line is they want whats in your wallet!
Just remember it's always about being informed and knowing that the service writers usually have no idea what they are talking about. They arent mechanics, they are salesmen. They want you to pay for repairs because they dont make money off warranty items and are pushed to make the sale pitch to the consumer.
I attached a couple links that go over the Magnuson-Moss Warranty act and its section on implementation of aftermarket items. To sum it up, if they cant prove that the part directly caused a failure, or that the part was improperly installed causing the issue directly, then the warranty by law cannot be voided on the remaining factory parts.
"..under the act, aftermarket equipment that improves performance does not automatically void a vehicle manufacturer's original warranty, unless the warranty clearly states the addition of aftermarket equipment automatically voids your vehicle's warranty, or if it can be proven that the aftermarket device is the direct cause of the failure.. "
"..a dealer must prove, not just vocalize, that aftermarket equipment caused the need for repairs before it can deny warranty coverage. If the dealer cannot prove such a claim — or it proffers a questionable explanation — it is your legal right to demand compliance with the warranty.."
also under the law is this little tidbit, just in case they ever tell you going to another mechanic other than the dealer will void the warranty..
"No warrantor may condition the continued validity of a warranty on the use of only authorized repair service and/or authorized replacement parts for non-warranty service and maintenance. For example, provisions such as, "This warranty is void if service is performed by anyone other than an authorized 'ABC' dealer and all replacement parts must be genuine 'ABC' parts," and the like, are prohibited where the service or parts are not covered by the warranty.
These provisions violate the Act in two ways. First, they violate the section 102(c) ban against tying arrangements. Second, such provisions are deceptive under section 110 of the Act, because a warrantor cannot, as a matter of law, avoid liability under a written warranty where a defect is unrelated to the use by a consumer of "unauthorized" articles or service."
Hope this helped. Now go get your headers.