On the 25-pin I/O port, you can connect your retrofit inductive proximity sensors as limit switches to circumvent the insufficient accuracy and homing repeatability of stall homing.
I don’t use a breakout board, as it may exert too much lever force on the 25-pin connector on the pcb (and is usually at a non-convenient location), but a 1:1 25-pin modem cable that leads to an aluminium case into which I mount the 8 mm cylindrical sensor sockets. Sensors can be Omron E2B.
The 25-pin I/O port also contains the RS-485 serial communications interface to control a VFD/spindle.
You already discovered the meaning of the ‘tool-enable’ pin (switching your non-spindle non-VFD milling motor on via a relay when M3 command is encountered), and ‘estop’ pin (to trigger the internal estopped mode which stops all motors and spindle (and unfortunately lets you loose all your positions and offsets – no one knows why 
)