Brad, when a timber frame designer make a set of decisions about a frame's design they are generally called "General frame rules".
These general frame rules are such things as 1)all joints are reduced to the next 1/2" down in size. 2)all joints are 2" off layout face and then 2" thick. 3) all bents are laid out from the west side except the east most bent. 4) braces are framed to 4" thick.
What this means (#1) is that all joints are reduced to a common size so that irregardless of the size of the rough sawn timber the joint is sized to one common size. So the tenon on the end of a 8x10 tie beam is sized to 9 1/2" and and mortise is sized to 9 1/2" and the housing where this tie beam enters a post is sized to 9 1/2".
What this means (#2) is that all joints are laid out from one of the reference faces on both the tie beam and the post, using the above example again. So even though the tie beam is 8x10 and the post is 8x8 the tenon and it's mortise is 2" off the layout face and then 2" thick. Also, the brace pocket in the tie beam and the post are also laid out to the same spacing. This keeps everything lined up and easy to layout and cut. This the value of square rule framing.
What this means (#3) is that irregardless to which way the frame will sit on the lot when it's raised, the designer has placed a compass north arrow on the plan and it is used to understand which way is east and which way is west. And the interior bents are laid out to this rule. This again makes it easy to layout joints and cut them.
What this means (#4) is that if you have a rule like #2 and you have 4x6 braces the tenon will be 2" off the layout face and then 2" thick. But the brace is 4" thick so what happens when the brace stock has shrunk while waiting to be cut? You can't move the tenon off the 2" offset. You can't make the tenon 2" thick as the stock has shrunk. So, what do you do?
You don't order 4" stock for braces; you order 4 1/8" stock or thicker. Then you have enough wood to layout your tenon 2" x 2" and then you shave the back side of the brace stock so that the tenon ends up 2" thick, using a hand plane.

So in your frame your chalk line will show you the 2" offset and all mortises should be on the line, if that's your "general frame rule".

Now in Jack's house the posts were oak, and therefor stronger so he used a different rule that the tenons on the oak posts could be 1 1/2" off the layout face and 1 1/2" wide. And as I have just reviewed his book and frame design again, it appears that most of the joints in that house frame are 1 1/2" x 1 1/2", with the exception of the scarf joint tenons. So that frame will have some general frame rules and some exceptions to those rules.

Standard timber framing rules for sizing tenons are that the tenon should be 1/4 the thickness of the timber. So an 8x10 tie beam should have a 2" thick tenon. And another standard timber framing rule is that the peg diameter should be 1/2 the tenon thickness. Now each frame has to be individually evaluated by a timber framing engineer to make sure the joints won't fail, but these are some standard rules.

Jim Rogers