Do you know of any research or science that demonstrates that? I would be interested to see it. I used to be a paid up member of the "its all in the pickups" club, but I've changed my mind in recent years.
The trouble with this sort of thing is that doing real science to demonstrate what is really going on is hard, and takes lots of money and even more time and commitment, so its rarely done. Especially if people are afraid they might not like the results. Plus when people don't like the results they usually try and discredit the research rather than change their preconceptions. It would interest me to see an experimental instrument built and carefully recorded, with, say, wood chopped off body neck and headstock until finally nothing left. Make a little machine to pick the strings in exactly the same place and pressure each time, and then the waveforms compared. Would they be exactly the same or would there be differences? Would the differences be sufficient to be audible to the average member of public/average musician/musician with particularily precise hearing? I have no idea, but, here's the issue, I am not so very interested as to be planning to actually do the science.