I have a tough time reading in depth articles on a screen. I do a lot better with print. Just found a reference to drilling and reaming  the front sight hole. Must be another 30 caliber barrel being described, not Krag. I had thought the threading was indexed to the barrel from previous discussions but these barrels are threaded first then holes are drilled for the sights. So after threading, the barrel would be screwed into a bushing with a shoulder to get it clocked or timed correctly. all barrels get screwed into the same bushing. As that bushing wears and timing gets off it could be corrected by rotating it to bring the timing back, that is assuming the machining order here is roughly the same as done on the Krag.
I think for the Krag, I would have made the dovetail machining and rear sight drilling as part of the same set up top avoid errors of moving the barrel between operations. But that is  based on the way I think not necessarily the way it was done.