This one is hard.

We know the SKREEM is decoding the FOB signal, because the SKREEM is flashing the turn signals.
We know that the CAN BUS from the BCM to the CLP//SSM is OK, because the console switch works.
We know that the CLP/SSM's pump is OK, because, again, the console switch works.

The driver's door lock cylinder is wired to the SKREEM, so if you unlock the drivers' door with the key, the SKREEM should tell the BCM, which then tells the CLP/SSM that an authorized unlock has happened and the alarm can be disabled. If you are not getting an alarm after unlocking the driver's door and opening the door, then we would expect the FOB to also work.

If you look in the service manual at the "Power Door Locks" section in the wiring chapter, you will see the control lines from the SKREEM to the BCM:

C4 - 57: Door Lock Switch Sense
C4 - 55: Door Unlock Switch Sense
C4 - 59: RKE (Remote keyless entry) Status

These pins are how the SKREEM tells the BCM when the FOB buttons or door lock cylinder are manipulated. I"ve never looked at these lines act in response to the FOB or key in the door. I may do a test or two this afternoon - that point is where you determine if the SKREEM is telling the BCM what to do, or not.