You can drill the holes deep, but I think 3 oz. top is a bit too much, because you'll be drilling out much of the top of the core.
I would go the route of adding a "fake" thumb hole. Drill the ball, fingers first, so that the pin is above or even with the fingers to avoid flaring.
Now you can drill a thumbhole in the ball, but it doesn't have to be very deep (an inch should do) or down very far like a normal span ball. All that has to happen is you palm must cover it. You should now be legal with your finger weight.
You can add a weight hole also if necessary or for leverage drillings and such.
You can have a balance hole with no thumbhole. In this case, you'll be using the center of your bridge for weighing up the ball. =:^D