I don't know if the transponder is different, within the engine ECU a transponder serial number either gets marked as a master or a valet. A key unknown to the vehicle is essentially neither a master or a valet, it is a foreign key.
To alter any configuration (add or delete a key) you must first have a known master key for the programming functions to work. Not just any key, but a key registered as a master within the ECU database.
One of the programming functions is to delete all keys and re-add the ones you have. This is a good thing to do, it means key that are not in your possession will no longer work.