I don't think that should be an issue. The keys can be coded to the car and the physical locks changed. The RF part will only activate the actuator on the lock surely, so the lock wouldn't need to be coded to the key. Unless the actuator has its own decoder but I doubt it.I agree with you, but I assume "the locks can't be changed" refers to the radio frequency and protocol the car is coded to receive before operating the internal locking mechanism.
They are coding a new set of keys to the car, where as they really need to be coding the car to a new set of keys.