The short answer is, it depends. The warranty coverage will range widely from dealer to dealer. The dealership will have to prove your modifications have caused the issue you are bringing it in for. The discretion will vary widely from dealer to dealer.
From our experience, most dealerships will care more about hardware than a tune. We also provide a stock file to flash before you go into the dealership for work. Our suggestion is also to speak with your local service advisor and see what they have to say.
