There probably is two kinds of plates. One is just a new surface for the gears to spin on. The other actually redirects oil flow for higher pressure, designed by Jim Ruggles. Sounds like you have Ruggles designed booster plate. I would do what the insctructions say, otherwise you won't get the benefits and may actually restrict oil flow. The hole isn't drilled in the plate, but in pump cover itself.
Where did you get the plate from?