I don't know - the only guitar I ever owned that had a pad under the plate was a TAG. So that's pretty telling in and of itself. I do know based on my own limited experience that simply loosening the neck bolts and reseating the neck can sometimes have a very noticeable affect on the tone/resonance/whatever. My best sounding guitar has shims in the neck pocket AND under the nut AND a loose neck pocket. By all rights, it should suck. And I've had guitars with perfect neck pockets that weren't anything special tone-wise. Some people want a neck pocket so tight that bolts are an afterthought.

Suhr will tell you that a neck pocket that is TOO tight is a bad thing.
It's hard to make heads or tails of it sometimes. At least for me...