What door conduits are you going with ?. The reason I'm throwing this out is some door conduits require different sized holes on the door versus the cowl side so keep that in mind.
If it is a finished car, once the holes are drilled out or punched, seal the bare metal edges.
If you can go with the large conduits so that what wires you need to run, as well as possibly terminated ends that might plug into things like the door panel window switches, power window motors, power door lock actuators, and such, now fit easily though the conduits and then in the future if more wiring needs to be run, the conduits can handle it.
A set I bought for a 69 Camaro project:
Jim