Any modification you do that causes a failure in your car will void the warrany as it relates to that failure. No modification completely voids the warranty on your car.
For example, if you install a chip and then have an engine problem, they may void your warranty if the chip causes the engine problem. They wouldn't be able to void the warranty on other parts of your car that aren't affected by the chip, though.
From a practical standpoint, any mod that increases the power your car makes could cause a failure in your drivetrain which wouldn't be covered under warranty. That could conceivably include the engine, transmission, and rear end.