It is all about pickup position. When a string vibrates, there are places across its length that are antinodes where there is no movement. If the pickup had a sensing point that was infinitesimal, there would be great nulls in the sound of certain notes. Lucky for us, the magnets in pickups that "pickup" (that's a verb) the string velocity have a wide sensing section along the length of the vibrating string. This lessens the nulls.
When you add another pickup to the mix, the location of it relative to the other pickup can result in cancellation of big chunks of the frequency spectrum. But is depends on the frequency of the note that is played.
However, if it were as simple as phase cancellation, you could buy a 30 band equalizer and turn a Tele into a Strat instantly (which you almost can). The difference is, the harmonic content of the string is quite high when first plucked, but then settles out to a pure sinusoid near decay. Since the harmonic content varies so much around a plucked string with 2 pickups that are placed apart by a certain amount....quack is born.
Here is a quack experiment of mine...
The Blue Tele