In school woodwork lessons, when marking a mortice, we were taught to define the start and finish of the cut by sighting the position of the marking gauge pins at each end of the pencilled rectangle and pressing down, all with the fence tight against the work, to make small but definite holes. Then mark the lines, with the pins falling neatly into the holes made at either end. Easier to demonstrate than describe, but the result was a nice clear marking with a definite start and finish, rather than a vague run-in and run-out.
It's not vital for all mortices, but avoids stray lines showing on the insides of stiles beyond the intersecting rails.
Is there an equivalent technique with a wheel gauge? Or must you remove the over-run with a smoothing plane?