Yes, it will be fine. I've got 4 or 5 balls drilled similarly.
All the pin is, is a marker. What matters is where it's placed relative to your PAP and the other graphic measurements (CG, MB) on the ball. For instance, if you want to drill a ball 4x4 and that ends up putting the pin "in" one of the holes, no big deal. Just drill it out.
Jess