I'd call the input more of a convenience feature for a takeover of a system with a similar arrangement or for a retrofit application. In a new install, I would recommend running the cable to begin with.
The output isn't really of too much use unless you use it as a voltage trigger or sink, as it's too "light" to support anything else without a relay. I commonly use them to drive the LED on external weigand readers to drive the red/green LED on a standard reader, then make appropriate rules to act like a normal ACS for lighting events. In the case of a reader, you're going to be interfacing either with the keypad (pigtail) or a KAM, but that's a different animal, so keeping the LED trigger at the keypad with the weigand data makes more sense.
Again, based on the additional hardware, I would recommend running the wire for a true output back to the panel.