It only asks for fob 3 if 1 or 2 is within range. Put those fobs FAR AWAY until the car asks for fob 1.
Like I wrote before, I'm not optimistic, but I haven't read about theft protection sensing the engine; it's usually the Bose Premium Info-tainment system.
The hood-latch has been known to set the theft systm. Maybe someone else has an idea for you.
Don't try to guess your way through this procedure. If you don't have a manual, do plan on getting one. There are links to free pdf versions around here somewhere.