Great questions. As you point out, I'm using the 0K resistors as jumper wires. It's a one-sided board so the 0K resistors basically act as a second layer on the board.

Regarding your first question, I am not sure how to place a component only on the layout diagram. This would be ideal, because the 0K resistors really shouldn't be encoded in the schematic.

I agree with your second point -- it's just an inconsistency in my schematic!