Currently the design assumes that the local controlling device will be driving the LED's And that the open collector transistor outputs will be used to drive the remote circuit.
However another use for the board is to provide isolation such that you don't have ground loops when working with analog data acquisition projects. In this case the remote device may still be a low voltage Arduino/PI/etc... but the open collector from the breakout boards are driving inputs on the local board. Think of desiring to monitor simple snap switch inputs and providing isolation to the project.
However because the BOB9118 has the grounds connected on the LED side of the optical isolators the only solution is to left the pad and run a jumper over to the unused pin on the header. It would be more useful to run each LED cathode to its on pin on the board and simply allow the user to decide to connect the cathodes together.
Another possibility would be to allow a simple cut on the circuit board to be made... unfortunately that run that connects the two together is done UNDER the opto-isolator. The only choice is to cut and lift one of the cathode connections on the chip... not a very clean solution.