Tune is emission intact Tuning, Delete is removing all ( AECDs ) Auxiliary emission control devices, Deleting if you live in CA would provide less risk, just make sure you have control over you tuning..
Tell the shop to enlighten us on how Broken Flex plate or TC adds metal shavings to the oil filter? I have never heard of a 3.0 broken flex plate. That shop is going to suck up your wallet and drain your bank account.