If the dealer can prove that the modification you did caused the malfunction that would be covered under warranty, they can refuse to service it under warranty. They would have a hard time proving that your aftermarket body kit, for example, caused compression loss in your engine. It's their burden of proof, if they don't have proof, then they would much rather honor the warranty then have a lawsuit on their hands. Intake, exhaust and tune wouldn't outright void the whole warranty, but anything that could be caused by those could be refused coverage, but they would still have to prove your mods caused the issue.