The dealership can decline your warranty for a number of reasons depending on how strict they are with claims. Personally I've never known anyone who's warranty has been declined due to a CAI or exhaust (5.9 truck), but they are a "gateway mod" which can lead the dealer to believe you have gone deeper with programming and fuel mods. Most modern CAI setups like AFE and S&B both exceed factory filtration specs and on the 6.7 even have mounting locations for MAF sensors and the filter minder, so I don't see any reason for a truck to be turned away for warranty work with either of those kits installed, the exhaust is self explanatory though.