Trimber,
I can see at least one situation where you would not use pegs driven at a nominal 90 degrees from the face and that would be where lap joiney is employed. Oft times, especially with cruck framing two pegs will be driven at differing and equally opposite angles to help lock the lap faces together and prevent separation of the joint, but where a mortice and tenon is employed i.e. a fully enclosed joint then this would not be required. Tapered pegs driven into an offset (drilled) mortice and tenon joint do not pull up and sit at exactly 90 degrees but at a slight angle reflecting the degree of taper on the peg since tapered pegs pull up tight on one "face" of the peg only
Regards
Ken Hume