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This begs the question that if these lines are created on the master hub, why aren't they apparent on more of the working dies?
Because the master dies and the working dies are both polished after hubbing and hardening. In almost every case these two polishing would remove all traces of the lathe lines. (Some polishing would also have to be done on the master and working hubs as well to remove the oxidation and scale from the hardening process. That should remove most of the lines on the devices.)
If the lathe lines were from the turning of the die bodies to create the shallow cone face these lines might also survive the hubbing since the fields of the hub would be the last part of the hub to make contact with the die blank. If the hub fields made "gentle" contact with the die the lines might survive.