This is certainly possible. As CES this year there was a car alarm maker promiting their latest system which would make a compleetly different chirping noise within 48 hours of a new key being programmed. The idea was that if you took your car in to a shop, someone would program their transmitter into your car and note your address. So by beeping differently, it would tell you this had happened. Being a college student, I essentially have two addresses 200 miles apart, so I always just give them my address 200 miles from wherever I am, which accomplishes pretty much the same thing.
My Honda prelude claims to have some imobiliser system with a chip in the key, but I've bought keys at the dealership without them programming them into my car. It didn't give me too much faith in the system. They did give me a cool red key and told me nevery to use it when I bought the car though.
Matthew