No.....it won't void the warranty. Read the Magnusson Moss Act sometime. Basically the owner and seller/mfgr have rights under a warranty but there has to be a direct link to an owner mod to the failure.
For instance: You put on a CAI. Your new truck's gauge cluster and front control module fail. Warranty applies as there is no direct cause of the failure by a CAI to gauge clusters.
For instance: You put on a Bully Dog programmer on your diesel and you run it hard, at the highest settings, exceeding maximum Exhaust Gas Temperature numerous times. The turbo fails. This is not warranted. The programmer has a direct link to operation of the turbo and engine by increasing fuel to the engine, creating higher EGT's.