The placement of pickups is actually a complex science of harmonics, but basically it like this: the more apart you place the pickups, the more varied sounds you have. If you place them too close together, you might not even notice the sound difference between pickups.
That's why people started adding more pickups than one. To have more tones to choose from.
Now, as to harmonics, a badly placed pickup can start blocking certain harmonics. For example, if you place your pickup right on the place of 24th fret, you lose your 4th harmonic. And the loss of even harmonics is the last thing we need.
Though the change in tone because of these harmonic changes might be unhearable, I don't know. I'm just using some theory to assume this.
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Jimbo