If they have computer techs working on the aircraft they could put in a legitimate transponder code, re-paint the aircraft, and do anything else to make it look legit. Then file a fictitious flight plan to the US and get into the system. No one would be the wiser among the many other aircraft flying on the NATRACK.
Transponder codes are issues by Air Traffic Control before each flight, they are not specific to an aircraft.
In order to get a transponder code, you have to file a flight plan and one will be issued.
Or fly VFR (1200).