You would be correct on the system operation. The passlock system uses the BCM in cooperation with the PCM to disable the car when the signal is wrong. There's no way to bypass this particular system. When the signal is incorrect from the key, the BCM tells the PCM to disable the fuel injectors (the injector drivers in the PCM are disabled.)
A dealership would be able to program the new parts using the GM MasterTech scantool, however, if there's a problem anywhere in the system, they will get the same results that you got.
How did you try the auto learn? Did you do it like this:
30 MINUTE LEARN PROCEDURE
1. Turn ON the ignition, with the engine
2. Attempt to start the engine, then release the key to ON, vehicle will not start.
3. Observe the SECURITY telltale, after approximately 10 minutes the telltale will turn OFF.
4. Turn OFF the ignition, and wait 5 seconds .
5. Repeat steps 1 through 4 two more times for a total of 3 cycles/30 minutes , the vehicle is now ready to relearn the Passlock Sensor Data Code and/or passwords on the next ignition switch transition from OFF to CRANK. IMPORTANT : The vehicle learns the Passlock Sensor Data Code and/or password XXXXX the next ignition switch transition from OFF to CRANK. You must turn the ignition OFF before attempting to start the vehicle.
6. Start the engine, the vehicle has now learned the Passlock Sensor Data Code and/or password.
7. DTCs will self clear after 100 ignition cycles.
The auto learn procedure is actually a 30 minute procedure. Follow these directions exactly
as I listed, and if there's no other problems in the system, the car should start after the half hour.