The RJ-11 port has a number of uses. Most common use is to default the radio when you forget the IP address or password of the radio. Inserting a default plug and rebooting the radio will bring up the radio with a default of 169.254.1.1 and no password.
The second option is for when you are aligning SM's. The RJ-11 Port used with a headset will emit a pitch, tone & cadence used to alignt. The third option is GPS Syncronization. The AP can be set to receive sync over the power port (RJ45) or the 6 pin port. The last option is for remote AP's. See below for details of the Remote AP:
