Brad:
I believe the way Steve Chappell designs his joinery is called Mill rule.
That is the timbers are true size 8"x 8" for example and all surfaces are 90° to each other. With timbers like this, the mortises can be cut right into the surface of the timber with no housings. And with all the faces correct it is easy to check your work and see that the joints are cut correctly.

In square rule timber framing the trueness or lack thereof of the timber is compensated for by cutting the joinery to an inner prefect timber of a smaller size, thus creating the housings.

These joints have to be done correctly based on the reference side and or face, and the adjacent face. And the dimensions are usually pulled from the arris where these two faces meet.
If the faces aren't truly 90° to each other then you'll have to use your layout tools to check your work to insure that the joinery is true. Or you can plane the joinery area to be true first.

Jim Rogers