Actually you want the hanger aligned to the cogs and not the wheel. Most use a wheel because most don't have a Shimano alignment tool and the wheel is attached to the cogs. The Shimano tool uses the hub's threading (as in the freewheel threads) to mount an arm that can be rotated around, taking the place of the rim. One shop that I worked for had a few of these tools, each on a hub with a different OLD.

But, again, most just use a well trued wheel. I do. At home this wheel is one of my building wheels and so is properly dished as well. BTW my rear triangle building wheels are laced on BMX front hubs. The axle diameter is 3/8", so to fit long enough axles for up to 145 OLD. And the dishing results in a symmetrical (no dish offset) wheel side to side allowing the sighting of the rear triangle alignment to be the same side to side. Andy.