There's a big difference between observing a difference and knowing what caused a difference. You can't say "A causes B", but you can say "I observed difference B after I made change A", then your statement is accurate and doesn't place any burden upon you to explain said cause. The fundamental is more energetic than the harmonics, that's a given, but what gives you cause to believe that the the flux of the fundamental is stronger, or has a further reach into the coil, than the harmonics? Keep in mind that the harmonics are riding on the fundamental since it's just the one string providing all of the movement simultaneously, so that when the string is swinging closer to the coil, providing a fundamental flux change, all of the harmonics are coming with it too, also getting closer in to the coil. I see no reason why there should be a change in proportionality between fundamental and harmonic depending upon either the distance of the coil, or the magnetic strength of the string. Bringing the pickup closer to the strings definitely creates a different tone, but I don't think it's because of a changes in harmonic proportionately with the fundamental, but rather the shape of the waveform changing as result of the flux being proportionately stronger when the string swings closer to a pole piece that is nearer. Magnetic strength decreases exponentially, so the closer the string is to the magnet, the more distorted the transfer will be, the further away it is the more linear it will be.