Hopkins
Commercial User
IME, necks definitely matter. On several occasions I've swapped different necks made of of the same materials on the same body and the tones varied quite a bit.
Player technique may be the largest but perhaps an easy variable to control. I know that how I play greatly influences the tone. I don't find keeping my playing technique relatively constant hard to do since it's practically the job title for bassists.
As far as sample size goes several hundred would give a better idea of any trends that may develop. But I seriously doubt that's ever going to happen.
So we're left with the personal experience of those playing the instruments. What doesn't matter to one player may matter greatly to another.
It would matter if I were trying to test the frequency response of the instrument on a scope, but in that situation everything would matter, including using the exact same electronics and hardware, and strings, and the pickup height and setup would have to be within a few thousands of each other. My test is human perception of sound, and the accuracy of the way woods are advertised. If the absolutes used to describe the sonic attributions of body wood are true, then they should be present even if there are slight differences in the neck wood. Setups will be carefully measured so each guitar plays the same, and the pickups will be at the same height. I will also test each pot on my multimeter to make sure the resistance is the same for each pot.