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Well the pickup not only vibrates differently, but pickups feature permanent magnets. Take a bar magnet, pluck a string, and move the magnet over the 12th fret, every motion makes a NOTICEABLE difference.
So when you're on stage, the amp blaring and moving your entire guitar, body amp, etc, the pickups are moving with the body, and moving the strings.
So when mounted this way, as mentioned earlier, the resonant peak changes.
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Please do not insinuate anything sexual from that.
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