An interesting range of responses. There are perhaps 2/3 factors at work here. The first is that boring machines are non-existant here. Those of us without chain mortisers are boring out our mortises with a power drill, often with no stand. Drilling guides can be found in some shops but in the 5 places I worked during my course I only ever saw one drill guide (A really nice Mafell with matching carpentry drill). I do notice when the bit passes through my pre-drilled mortises, but it's never posed a problem. Obviously with a boring machine losing the lead thread might be more of an issue.

Secondly, I was taught "standard practice" here and a standard roof truss here is made from 8x23 (75mm x 225mm) timbers. A 30mm wide mortise in a 75mm wide timber leaves you with ~20mm each side of the mortise. An alignment issue will blow out the fibres as the peg exits the tenon. I've seen it done a few times.

Tim: I wouldn't call it a hang-up. My post stemmed from the fact that my personal experience led me to find this to be a better system. And having a routine is not a hang-up. Your routine is to bore peg holes after. Jim does it just before raising.

Don: It's not necessarily about being perpendicular. It's about alignment. A mis-aligned peg hole can put more pressure on one side of the tenon than the other, or cause blow out of fibres on the exit side. But in large timbers this is rarely an issue (the peg just gets stuck).

What I really find interesting about this is that each person seems to have their own reason for drilling pegs holes after cutting the mortise. Which suggests that it's not a universal system because it's taught that way, or at least everyone has found their own justification.