Good point and especially important with certain pickup designs like the MFD pickups on G&L basses and others of a similar design using stronger magnets. All pickups tend to have their own “sweet spot” and while it’s best to have a set starting point it’s our ears alone that tell us most about when we’ve hit it.
Our playing styles and setup will also have an impact on pickup height. If you tend to play hard and/or with a pick you may find lowering your pickups helps. Conversely if you raise your action then also raise the pickups to maintain their same distance from the strings. String type and gauge will also have an impact on the “sweet spot”. So experiment with pickup heights 'til you find that.
When I got my bass the E and to a lesser degree the A were both way louder than the D and G, regardless of tone knobs. A few googles and a few turns of the screwdriver and all was in harmony.