They would still need to turn the ignition on. Some random key from Japan will not work in your ignition switch.... but the pros can bypass this pretty easily as well.

 

Oh and by the way OP, If you don't want to modify that key to hold the transponder, you can keep it separate and will just need to hold it near the key when you turn the ignition on. Once the car has started it doesn't care about the chip. You could just make some kind of protective case for it and put it on your key chain. Find a plastic or rubber key chain ornament and put it in there.