Pickup height is often treated like decoration: raise it if the guitar sounds weak, lower it if it is too loud. On the bench, it is more connected than that.
Magnets interact with strings
A pickup that is too close can pull on the strings, change sustain, create weird overtones, or make one string overpower the others. A pickup that is too low can sound thin, distant, or uneven. The right height depends on the pickup, the guitar, the string gauge, and the player.
Balance matters more than numbers
Factory measurements are a starting point, not a finish line. A bridge pickup, neck pickup, P-bass split coil, humbucker, Strat single coil, P-90, and active pickup do not all want the same treatment.
Setups should include listening
A good setup is not only action and intonation. The guitar should also be plugged in, balanced across pickups, checked for string-to-string volume, and adjusted so the electronics match the way the instrument is played.