Jed,
That is exactly the way I was taught to do it by Jack Sobon. Peg holes are laid out and bored as each timber is completed. No "double-assembly" required. To keep the peg holes square to the timber while boring, set a couple of combination squares on edge to sight against. After a while your eye picks up the relationship between the bit and timber.
To be sure you are drawboring in the right direction, move the tip of the bit on tenon in the same direction you want to "move the mortice", i.e. towards the shoulder.
Is it the best way? Possibly for some, but not for others. Like many things there are several ways to do it. It's still possible to make mistakes, but in my opinion, no more so than any other part of the layout process...
Cheers,
Dan
