I did a deep dive into the tune after the flash and all it does is change the throttlebody and start and stop, the cats are bigger than stock or what was before the recall so I think the engine breathes better, And you get a whole new set of O2 sensors. If I were you I would get the new mechanical parts but tell them not to flash the PCM. If you have to put a cap on your OBD2 port. That is if you must have this done, otherwise ignore.