How far from the flange (or from the center of the axle) was the damage? Did it line up with the rivets?

Brandt's book talks about one minor difference between stringing the DS spokes inside-out or outside-in. The hub actually twists a little such that most of the driving torque is applied on the DS, and the pulling stress will tighten the trailing (on the top) spokes. This straightens them out a little. If they are threaded head-out such that they cross to the outside of the leading spokes at the last crossover it will pull that spoke intersection to the outside and reduce clearance. It isn't much and may not matter on any particular bike. Lots of wheel builders build that way. But with a tight clearance it can matter.