I've pondered this before as well... my not-so-educated guess is that it all boils down to the string vibration being the only thing a pickup can detect. Since the pickups are only sensitive to disruption of the magnetic field, it doesn't really matter how they're mounted. If you've heard any of Paul's talks on guitar physics, his theory on trying to approach 6-in-6-out, the goal is keeping the "system" from taking away from the energy of the strings. In the guitar, the nut, bridge, wood, everything is trying to preserve and sustain the energy of the string vibration. But pickups don't detect vibration of the guitar itself, nothing in the guitar aside from the strings can change the magnetic field. Vibrate an unstrung guitar or pickup while it's plugged in, I doubt you'd hear much of anything, at least you shouldn't if it's a good one! The only thing a pickup can report is what the string above it is doing, the magic in the guitar tone is keeping that string dancing.
And now, I'll crack a beer and wait for someone that knows a lot more to prove me wrong. I'm keeping one hand ready for the facepalm...