I read about this in depth when it came out. I do not know why they have you bring in your old keys, but they do not re program them. I think they make sure your keys are programmed into the RF hub before they lock it. And they offer you a one time discount to buy additional keys because the red ones are quite expensive. Once the hub is locked you cannot get new keys made for your car.
Once they lockout the RF hub the thief's can still use the star connector to get to the RF hub but the RF hub will no longer accept their instructions to program a new key into the electronic device they are using to attempt to steal it.
The IGLA anti theft system does the same thing but does not destroy the RF hub. When you leave the vehicle the hub is locked and they cannot program a new key to steal it. When you get into the car you type in your code on the steering wheel, and the RF hub is unlocked and you can drive it AND have new keys made later if you lose them.
So in effect the RF hub is much cheaper than buying the IGLA but you do not get the other anti theft features the IGLA has. Personally I have the IGLA system and keep my car in the garage at night, and am not afraid to use it daily for shopping etc. If it gets hauled away on a flatbed I have it insured for $90G and will then buy a GT500 and not have to deal with this bullshit anymore.