According to law that only way a warranty claim can be denied by the use of aftermarket parts is if, and only if, the use of that part causes the warranty claim.
For example, you put a supercharger on and blow your engine. You are not going to get that fixed under warranty without any problems. Assuming you show up at teh dealer with the blower still installed
If you are running a set of duals and you lose a headgasket they'd have a hard time denying your claim. That being said if they did deny the claim you'd have to go to court, assuming you run up the chain at Ford and get it denied the whole way.
So the legal answer is no, but the realistic answer is maybe, depending on the friendliness of your dealer and your willingness to play hardball. Oh, one other thing, the OEM 10 year warranty on the exhaust mandated by emissions laws would not apply on all the aftermarket parts, not sure about the OEM stuff left after adding duals still being covered. A strong case could be made that the addition of non-factory approved parts to the exhaust system caused the failure of the remaining parts of the factory exhaust and in any case they'd only be obligated to return it to original condition.