I think I get what you’re talking about. I had a similar idea myself when I considered the 4g69 into ce chassis. In the CE, there is separation between what I call the body loom and the engine management loom. Ie headlights, door locks, interior lights, windows are not tied to the ecu. This is proven by disconnecting the ecu.
However... pretty much all of the wiring comes through the firewall together at some point, so the harness’s are physically taped together and possibly even use the same plugs somewhere, so it’s not as simple as it first seems. I think you will find with the motor out it will make more sense.
The other tricky bits I have not figured out is the A/C switch and the SRS control unit. They might need ecu access but I am not entirely sure as I sold my setup rather than completing it. Fuel pump wires and o2 also run alongside rear body wiring from memory too.