I see a basic problem in back-propagating 0Rs from PCB to schematic. There can be no wire directly corresponding to the track you break at PCB with 0R to break that wire and place there a resistor. And total rearranging a net at schematic is enough complicated task in my opinion just to left user to do it.
I am using 0Rs to avoid breaking my GND layer at 2 layer PCBs. At this PCB there are 2 0Rs at VCC net (other that can be supposed as 0Rs are ferryte beads):