I am backfeeding a 200 amp service with 4/0 AL XHHW conductors in a 2.5" Rigid PVC conduit to a J-Box and then continuing through the basement with SER. I would like to run the 1/0 CU GEC with my subfeed conductors through the PVC. At the J-Box, the GEC would continue to the water pipe. The water pipe is located in the same direction as the 200 amp subpanel. Are there any NEC rules prohibiting this approach?

I guess I'm obtuse today because you are not making sense to me.

The NEC requires that the service entry conductors connect with the Main Service Panel as close a possible to their entry point into the building.

Next, the NEC cites the cold water pipe as the primary grounding electrode and requires a supplementary ground rod.

The connection of the EGC must be within 5' of the entry point of the cold water pipe and to qualify as an acceptable the metal cold water pipe must extend at least 10' into the earth.

Can you tell us if you are trying to set up the main service panel or running a feeder to a secondary panelboard.

There is no restriction to do as you plan, just be sure the GEC is continuous, with no splices.