Allow me to present a general case where there is both consistency in layout and a variety of appearance by use of offset tenons and predictable layout of mortises. Suppose we are building a barn with vertical siding nailed to wall purlins (4 x 5) at 24 oc flush to the frame and has bracing (4 X 5) in set 2 inches quarter lapped with the purlins at their crossing. The posts are marked out for a series of mortises 2 and 4 inches from the reference side (the building line or the outside surface of the frame) for the braces, wall purlins and wall girts. The flush members will have the tenon cheeks marked at 2 and 4 like the mortises and so getting flush members. Since the brace will be inset 2 inches the tenon cheek will be marked only 2 inches from the brace's outside surface. The quart lapped joint will be marked at 3 inches from the purlins outside surface and the brace will be marked for the lap 3 inches from the building line or 1 inch from the brace's outside facing surface. Basically all this is managed by ALWAYS having in mind the building's reference planes. All the mortises in this scenario will be in line but the position of the members is dictated by the location of the tenons.