Facing the BB shell or head tube simply ensures the two faces of the shell or tube are parallel to each other while in the same plane as the threads of the BB or the tube of the head tube. It does not mean the threads are cleaned up which is why every shop that faces a BB shell will chase the threads first to ensure they are clean and the facing tool threads in without cross threading. This process does not ensure the frame is aligned.
Anyway, when I built my frames using Henry James BB shells they never really needed to be faced. After skimming off the paint layer I never had to do more than a single rotation of the tool to be shaving metal off the face all the way around the BB. His lugs and BB shells were extraordinarily high quality castings.