Hard endpoint where it gets reflected andYour description starts out OK. The snag you hit is the hard end point assumption - if it were a hard end point, you wouldn’t have dead spots.
The neck on your bass is a mass loaded bar, with distinctly assymetric end masses, and a non linear cross section, made of a very non isotropic material (wood). It has resonances (multiple frequencies where it resonates), and where the nodes and antinodes line up with the end point of a string trying to resonate at the same frequency, you get variations in how long the string resonates. When you get a combination of neck position and string tuning with a very short sustain time, we call that a dead spot.
Note that the dead spot is a result of two resonances (the string and the neck) at the same frequency. If you change either - by retuning the string, or by changing the mass loading at the headstock, the dead spot can moved or minimized practically. I have basses where I needed lighter tuners to make them work well, and one bass where I needed heavier tuners - it's tuned in D standard, so it called for a different solution. It had a dead spot on the open G string (the location where you usually have an A string), and the added mass was needed to move the dead spot down in frequency.
phase inverted;no phase inversion,no phase
cancellation,no dead spot. I understand how
increased mass lowers the frequency,decreasing
it raises it. How is a notes volume,sustain and
harmonic content diminished if it isn't partial
phase cancellation? If you agree that it is but
not from the machine head could you describe
the signal path. Where and how is energy being
taken from the string? Inquiring minds want to
know.