Never heard of somebody simply drilling a set of holes in the standard gear case to make a low water pickup. I have the CLE gear case with the low water pickups built in, and there's a whole lot more to it than simply a set of holes. There are actually a set of removable (to clean out weeds) plates on each side just below the cavitation plate too. I'm not even sure if those passages exist in the standard gear case.
On a related note, most aftermarket nose cones that include a low water pickup include a set of external braided hoses to get the water from below the bullet up to near the old (standard) pickup point.