It’s more difficult for those of us wiring things “in the field” from assorted retail parts than for a manufacturer with known sources, because we have no control over color codes / connectors / orientation. AFAICT, the least awful way is to wire (retail) things consistently, then fix it in the mix.
So you set Limiter Polarity to match whatever switch you just installed: True for NC switches, False for NO switches. When it’s set correctly, the input signal will be active only when the switch is pushed.
Then you pick Direction Polarity so the axis moves toward the switch during the homing operation when the controller resets. There seems to be no other configuration for the stepper driver DIR signal. Given the random colors and orientations of stepper motor wiring, there’s no way to tell which way it will rotate before connecting it and trying it out.
Finally, pick Invert keypad direction so the axis moves the way the control panel buttons suggest. This also controls how LightBurn moves the axis: both should go the same way.
Repeat for all axes and it’s all good. Maybe …