"re-routed the bridge hole a little more forward" = Nope, that's exactly what I did and whilst it solves the intonation problem you're left with a gaping hole behind the bridge.
"Could have shaved off the neck heel" = Possibly, but one; 6mm off the heel would look really shitty so close to the 21st fret. And two; the neck screw holes were already drilled, so drilling another 4 holes would severely compromise the integrity of the neck.
A lot easier just to get a body without errors in the first place.