I think you are missing the point of square rule joinery. The whole idea is that differences in the dimensions of the timbers are accomodated by making all of your measurements from the two reference faces and housing your joints. By housing your joints, you are effectively squaring off your timbers, but only at the joints - it is not neccessary to do it anywhere else.
You may find the discussion of square rule joinery in Jack's other book to be helpful.
Regards,
Dan
