If using a dishing tool you are measuring/indicating the position of the rim relative to the hub (actually the outside face of the lock nuts). The only way the spokes figure in this part of the wheel building equation is that they are the mechanism by which you will move the rim relative to the lock nuts...so it does not matter if the rim is drilled centered or offset for the purpose of establishing a properly dished wheel when building the wheel.

The offset drilling comes into play when choosing components to build with as it will have an effect on how much dish a wheel will have, meaning how symetrical or asymetrical the rear wheel will be when finished. This also impacts spoke length. But this has no affect on the process of centering the rim between the locknuts or "dishing" the wheel.

-j