I have heard that some people bore the peg hole before hogging out the mortise wood.
However if the frame is going to sit for a while, as the joints are being cut part time, nights and weekends, it is possible that the hole will/may distort when it drys.
I usually cut all the joints and then during my fit up testing of the frame, bore the peg holes.
This works for me.
I feel that the peg hole beyond the second side of the mortise is not that critical and if it wanders off a little it's not the end of the world.
Jim Rogers