When I first got my p/p, I snugged up everything. I didn't notice that it's tone was especially different. After I read this stuff from Buddy and Bobbe, I backed off my neck screws at least a quarter turn (my silver screw heads are clearly visible). I then thought I heard better sustain, especially on the high frets, a more trebley sound overall, and better string separation on the low strings, because their overtones were coming through better. Maybe it was all in my head, or maybe as I played the guitar longer I heard it better.

But all this does make some mechanical sense. There is general agreement that wood necks sound darker, and it is believed this is because the solid wood neck screwed tight (or glued) to the body essentially becomes part of a thicker body that is somehow deader. The metal neck is hollow, and so doesn't make much contact with the body. Possibly if you snug up the screws it maximizes the contact and deadens the tone a little, and as you back off the screws it minimizes the contact and livens the tone up a little.

Conversely, of course, the results of some neck/body combinations may include some ear-pleasing reinforcements and/or combinations of some vibrations, including beat frequencies, and it could well be that "tuning" the neck screws allows you to optimize that.