It's based on the same analog technology as the BMS Stage1, only instead of being set to 3.5psi as the Stage1 is, they set it to 4.5psi. BMS prefers to have CAN bus access in place for the higher boost levels so keeps those for JB4 level performance.
FWIW awhile ago BMS added the DB9 port back to their Stage1 tune so technically it can be adjusted from 0-6psi using the Stage1 interface and USB cable. So to match it up with the AFE set it to 4.5. The better solution though is to add the extra wires and JB4 box at that point.
The rest of the connections on the harness are meant for upgrading to the JB4. The idea is you just swap the box out for $150, connect the extra wires in the harness, and have a full JB4.
Mike