A guitar can measure well, fret cleanly and feel comfortable, but still sound wrong through an amp. That is why the last part of a setup is not just ruler work.
Pickup height, output balance, scratchy controls, cable noise and switch behavior all matter. If the bridge pickup jumps too loud, the neck pickup is muddy or the tone control cuts in and out, the setup is not really finished for the player.
The bench check has to include feel and sound. A guitar is a tool, not a spreadsheet.