Hi Tim,
It is the mortice face and tenon shoulder that does the work in a mortice and tenon joint and thus the face to face mating should be well aligned even if a hewn surface is the start point. Mating faces should be regularised (flatened) to provide reliable reference points that can then be transferred by scribing to create the mating tenon shoulder face cut lines.
Regards
Ken Hume
"Mating faces should be regularised (flatened)...
sounds like the begining of square rule, doesn't it?