I did a little research and the immobilizer looks to be a separate part from the key lock/barrel. It plugs into the lock with a short cable and plug that runs under the frame glove box. The question is, is the ICU or immobilizer control unit as it is called in the KTM parts list being programmed to the keys and giving the ECU the OK to start and thus maybe able to be fooled, or is it sending the key code to the ECU and might not be able to be fooled with a resistor or dummy plug. This part is listed a being for the 990SM since 2008 as well and list price is around $450.
A mangy man chasing a cautionary tale
KTM 990R 500EXC