If my most recent tinkering experience has any say in the matter, then yes, it matters. I was hooking up a J/MM set of Delano pickups and, rather than breaking out a ruler, I just let them sit a little closer to the strings than I usually do. Once I had the truss rod and string height set to what felt and sounded fine, I started plucking away with one hand to see what sound I was getting. Then, I pushed the pickup a little bit deeper into the body with the other hand to hear what a lower height sounded like. When I found something that was a good mix of thump, growl and clarity, I adjusted the pickup screws according and then called it a day.
If there was any "scientific method" at work, it wasn't because of any numerical value. Instead, I decided to go by what looked and sounded decently playable as a setup experiment. The only tools I used were the appropriate allen keys, a screwdriver, a tuner and my eyes & ears.

If there was any "scientific method" at work, it wasn't because of any numerical value. Instead, I decided to go by what looked and sounded decently playable as a setup experiment. The only tools I used were the appropriate allen keys, a screwdriver, a tuner and my eyes & ears.
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