First thing to understand is that the pins on the PMDX-416 are predefined as either Input or Output type. You must assign output signals to an Output pin type.
The set of Output pins is: 1, 14, 16, 17 (general purpose), and Relay (dedicated). There is also an internal dedicated signal for PWM speed control via a PMDX-407 spindle control module that mounts on top of the PMDX-416. It is configured in the SmartBOB plugin control panel Spindle Config tab, not the Output Signals tab in Mach4.
The set of Input pins is: 11, 12, 13, 15 (general purpose isolated), A, B, C (non-isolated, typically used for encoder inputs), and dedicated isolated inputs for E-Stop and Fault.
You cannot use pin 15 as an Output because it is an Input type pin.
Once any Output pin has been assigned, it will no longer be in the drop down list because only one signal can be allowed to drive a pin due to electrical conflicts resulting from multiple sources fighting to control the pin. If you are trying to use an Output pin and it does not show up in the drop down list, go the the Configure > Control > Output Signals tab and scroll down through the chart to be sure that there is not already a signal trying to use that pin.
Input pins CAN be assigned to multiple signals because each signal can observe the same pin without causing an electrical conflict. This is useful when you want to wire multiple limit or home switches to one signal. If you do this you must not move multiple axes at the same time while homing. You can also define the same input to be observed as a Home signal and as a Limit signal for that same axis.
Also, the list of signals in Mach4 can be confusing because some signals will have both an Input and and Output style functions. For example "Motor 1 Home" is an input signal that Mach4 observes while homing that motor. Depending on your axis assignments that motor could be the X axis. There is also an Output called "X Home" which Mach4 uses to tell an external indicator the status of homing. That Output signal is not required and not often used. I suspect you are confusing the "X Home" output with the signal that you need for Mach4 to monitor your home switch.