Pickups aren't microphones
You here a lot of talk about tone woods and resonance. But wait, the pickup is not a microphone. It is not picking up air vibrations. There is a vibrating metal line (the string) that is interrupting a magnetic field. How could the wood effect the output sound? Actually there are two ways it effects the sound, two very important and significant ways.
1) The wood of the guitar, the neck, the frets, the bridge, even the weight of the tuners effects the resonance of the guitar. The way the rest of the guitar vibrates effect how the string vibrates. Its all connected. When an A note is played there is a dominant 440 Hz vibration going on in the string. But there are also many harmonics of that note in the vibration. The guitar components will effect the strengths and weakness’ of various harmonics thereby changing the vibration of the string which is being “measured“ by the pickup. 2) The other factor is that when the string vibrates it causes vibration in the whole guitar. The pickup is part of that guitar and therefore the pickup is vibrating. So the magnetic field that is picking up the string harmonics is vibrating also. On a Stratocaster type guitar where the pickups are mounted with springs on a piece of plastic pickguard the effect is minimal. This is why Stratocaster type guitars have such a pure sound. On a McNaught guitar where such engineering has gone into the piece so that the pickup is mounted directly into the piece of wood making up the neck joint this gives a more pronounced difference. It is part of why the McNaught’s have such a uniquely sweet sound.
So you see, when a string vibrates the whole guitar vibrates and therefore effects the string vibration. It also effects the pickup by vibrating it. Get it?!