You are feeling the resonant modal frequencies of the neck. When string vibrations at the same frequencies excite the neck to vibrate at those modal frequencies, those vibrations are lost from the strings, so not seen by the pickups. That's the Conservation of Energy Law. It has been verified in measurements of real electric guitars guitars for some decades. And those losses can rise to a level sufficient to create "dead spots". But most losses are fortunately small, or electric guitars would not have superior sustain to acoustic guitars (which rely on vibration transfer to the body in order to be heard). You could of course "like" the overall sonic result of those losses from the strings to the neck, but neck vibrations are not obviously a "good" thing.
The skin mechanoreceptors via which we feel these neck vibrations are highly sensitive to particular frequencies. They can also be subject to "after effects", where their sensitivity changes over time (ask anyone who works holding vibrating machinery). So we can easily be misled as to the real magnitude of vibrations we feel (often overestimating magnitude, and feeling some frequencies but not others).
Oh sure... play the Science card! I prefer to live in the world of 'magic' and superstition.