Good point. Just a bit of clarification...

The axle doesn't really have to protrude past the edge of the DO, just go far enough into the DO so as not to slip up or down. If it protrudes past the outer edge of the DO at all it might stick out so far that the skewer clamps onto the axle instead of the DO. This means the bearing cones aren't positioned correctly so that the axle is too far to one side. When one side doesn't go in far enough the other side might stick out too far.

One cause of this could be that someone removed both cones from the axle when cleaning the bearings, and didn't quite get them in the same place when putting them back on. If you ever loosen both cones, measure the distance from the locknut outer edge to the axle end so you can get them back on in the same place.

Another likely cause is switching a wheel between bikes which require a RD claw vs. having an integrated hanger on the DO. Curiously, this is rarely discussed here in C&V.

Forged DOs with an integrated hanger are thicker than stamped DOs without a hanger. Stamped DOs have to be thinner because the axle has to go through the claw which isn't used on forged DOs. But that extra thickness is all on the right side. So the axle has to be positioned further to the right (or the bearing cones must be positioned further to the left on the axle) for a claw used with stamped DOs. Unless the axle is quite short a wheel will work on one or the other but not both unless you reposition the bearing cones as required.