In general, I would base it on each ply not the entire beam. If you were to place a screw exactly between two plies, I think the screw would tend to pry the plies apart. I doubt you would get good thread engagement which would limit the screw capacity, and by prying the plies apart, that would weaken the beam. Based on carpenty/construction projects I've done, having set screws between plies (by accident) I've observed this.
If the beam plies were held together really well (like by through bolting plus glue) then perhaps it's not as big a deal, but I would probably still try to avoid this.