That is a *very* neat way of doing it. Neat, and precise. It's like a proper engineering solution!
I guess the problem is "drill bit wander" - ie the bits don't drill through perfectly perpendicular to the top?
To counter that - and it doesn't sort the problem, but it does hide the issue - the other way I've used in the past is to drill the outside holes (ie upper & lower E strings) all the way through, front to back. Accept that the bit might have wandered a bit.
Then draw a line to join up the centres of those holes and measure positions of the holes for the other 4 strings. Drill from the front, just over half way through the thickness of the body, then flip over and drill from the back, again, just over half way through.
The holes will generally meet up in the middle of the body, at least enough for the strings to pass through the hole.
That way you have a neat, straight and equidistant, line of holes on both the front and back of the body, even if they're not all in exactly the same positions. You'd never spot the positional differences just be looking at them.
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