To the best of my understanding, it is a matter of tonal preference. Setting the pickup closer to or farther from the strings affects how they pick up the signal (stronger or weaker, maybe different ends of the frequency?). Some guitars come with the pickup staggered so that they will pick up the signal in a certain way. So it's no big deal....if you don't like the sound, raise or lower it until you do.
The closer the pickup is to the strings, the more powerful the signal will be....so if it's too strong on the treble, move it farther away from the high strings....too weak, move it closer.
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