No, DK, you use one of the shown (or variations)lay-outs. Both pieces of the stock are "drilled/mortised" the same and in alignment. There is skill involved, however, not nearly as much as if you tried to make the tenon/pin a tight fit. Drilling from the stock face does allow for a tighter fit and reduced glue line thickness (a potential source of weakness), but is not always practical. Maintaing hole location and alignment across a boundary (the break) between two separate pieces is not easy, but is, still, a basic machining function. Avoiding breaking through the outter layer of wood, the "skin," is also a skill. There are times for each of the basic layouts; knowing which will serve best is also a skill.
