I'm wondering whether some of the perceived difference in sound between a bolt-on and set neck (aside from the constituent that might be ascribed to general Fender vs Gibson differences - principally scale length and ferrous vs. magnetic pole pieces) might be down to stress? There's a big difference in that on a bolt-on neck, the bolt is exerting a constant force to hold the neck and body together. Even when you take the strings off, that immense compression in the neck heel and neck pocket is still there, an invisible By comparison, a set neck joint (once you remove the clamps) is no longer under that compression. It doesn't still have that internal stress in that area, just the tension of the strings and truss rod orthogonal to that plane. I'm not saying this is a problem as regards stability for bolt-ons, after all the way the neck and truss rod design vectorises and balances these internal forces in that plane is surely a fundamental part of what makes a guitar sound a certain way. But could it be responsible for some of that tonal difference we love to tell ourselves we can hear?