I was thinking the same thing as obviously the dealer gets paid either way whether from customer or FCA however I'm guessing if from FCA its the bare minimum reimbursement so if at all possible a crappy dealer will pass on a repair to a customer?I know others have already said this, but that dealer is full of it. I'm not sure any dealer can be that ignorant of the history of this engine, and if it were me I would accuse them of fraud.
They know about the AEM, they know it's covered by the warranty, and now by a recall. But they see that you are an uninformed consumer and they are trying to take advantage of you.
It seems likely to me that they would take your $6000, do the warranty paperwork with chrysler and pocket the warranty payment too. "Hey, double payday for us, and the idiot customer doesn't know the difference!"
make sure your FCA customer care rep knows all this, and call out the dealership on it too. Very Loudly, In the middle of their showroom, so all the other customers hear
Edit: I want to clarify from the above that I don't think you're an idiot, and I hope you're not offended by my post. By your own admission you're not mechanically inclined, and don't fully understand what the dealer has explained; but your intuition told you something didn't seem right and you came seeking more experienced advice. That alone puts you head and shoulders above the truly ignorant who will take it in the shorts and walk away smiling.
I only hope the advice and knowledge you find here can help you resolve this and any future issues.
Bring the AEM paper work in and show them where it states this crap is covered.