My problem with a notch from a knife is that my saw tends to want to center in the notch - if I've marked if from the mating piece, this ends up making the resulting pin too loose a fit- I want to cut just outside that line, not centered on it. So I either mark lightly with the knife or use a pencil.
How are you handling the offset issue if you're making heavy marks to guide the saw?
" Be willing to make mistakes in your basements, garages, apartments and palaces. I have made many. Your first attempts may be poor. They will not be futile. " - M.S. Bickford, Mouldings In Practice