From the master Carl Pedigo himself
"
One is not able to get the string thru holes to line up with wherever the strings dictate as perfectly as we'd like. So we prioritize the position of the bridge.
Back in the day we would position the bridge after the neck was fit. That allowed us to simply drill holes in the exact spot the bridge landed on. Presto! Perfectly orthogonal string thru chases. However, a slightly angled string path through the body allows for a little more contact ( string to wood). There are no downsides to a slightly angled string thru hole and a negligible advantage.
In the past we stocked MANY bodies in the shop so that one was ready any time a neck popped out. Now, everything is made on the same nc mill; so we make bodies then necks. (Or vice versa). While the bodies are being finished the necks get fretted.
There is no longer an opportunity to apply the bridge prior to finishing the body. As a result the string thru holes are at times a little angled.
We use a very accurate fixture to determine the placement of the bridge, once the neck is fitted properly, so that they always end up in the correct spot irrespective of some small string thru ferrule offset. "