So what happens when everything you believed to be true has been proven false?
You retreat to the comfort of string theory where there are equations to describe any universe you can imagine. There’s one out there where it really is the tone wood. And another where it’s in the fingers.
And in all of them, the pedals matter more than anything else.
Well, here's one bit of experience I've had. I used a cheap neck on a project, and it sounded like ass. I used a good neck on it, it sounded as expected. Good materials generally let whatever is making the tone do that job, bad materials can definitely take away from that.