Just a slight touch with a large countersink will do the job. If you don't have a countersink, you could touch it with a larger twist drill. Maybe use a 3/8" bit over a 1/4" hole or 1/2" bit on 3/8" hole.
I've never done this step. Old furniture used smooth dowels. I don't think Fluted factory made dowels were available until the '70's.
Dowels have improved and glue has improved.
There are so many ways to join lumber, it becomes a personal favorite for choice.
Dowels, Kreg system, domino, mortise and tenon, biscuits, etc, etc.
If you don't have time to do it right the first time, when will you have time to do it over?