So the difference was adding a second, separate conduit pipe - as opposed to using one for all the wiring? Is it a safety/code requirement?

Chris --- Good question! As our inspector explained, there are two reasons for the second pipe. One is immediate safety --- too many big wires together in the same pipe may overheat. The other is long-term safety --- with input and output wires coming out of same pipe, you can't tell if the box is properly wired. If improperly wired, turning off the main shutoff switch would still leave juice flowing throughout the box --- bad news!