For one, we never quite managed to convince people that the wiggly bits of metal were an important secret that should not be photographed. Cryptography can in principle be harder to duplicate/impersonate. (If, and big if, it's implemented correctly)
I mean - why don't we just integrate the dongle signal being necessary to unlock the car into the existing process and still require a physical key. As a bonus the key could be designed to interface with the car to communicate any signing tokens over a wired connection in the key socket instead of having any radio/wireless capabilities at all.