My intuitive guess here is how the ports are connected to the T2 security chip. One port is as you said a console port that allows access to perform commands to flash/recover/re-provision the T2 chip. Same as an OOB serial port on networking equip.
The rest of the ports the T2 chip has read/write access to devices connected to it. Since this is an OS drive, I'm guessing it needs to be encrypted and the T2 chip handles this function.