Hi Tim, I have seen recovered timber from a barn that had to get out of the way of a grocery store that had step rafter housings aligned to a red line on a plate. Other than that I think that the hewn timber was rough hewn in the woods, delivered to the work site and was corrected to a good enough state, I'm sure the lead told the men, "we ain't building a pie-anna." The cross grain layout would be striked with an awl against a large try square. The awl would be held in the groove of the story pole mark and the square brought up to the awl, the square held tight to the story pole and the awl is lifted off the story pole and then the line is striked. The gains are marked with a gauge set to the story pole. The story pole will bridge the undulations in the hewn beam. The other carpenter like solution could be a straight edge board set the dimension of the gain is aligned to the reference side and gains are marked with an awl. No caulk lines are really necessary with good enough timber. This is my conclusion from staring at old timber.