it's really just a preference thing (short of the point of playability issues if one shifts the neck enough that a string keeps rolling off the edge)
there's probably variation in center-to-center vs string edge-to-edge in the same way that some locate nut slots differently
it's interesting that you're getting a noticeable difference in sound with the subtle neck shifting--if you dig it a certain way and it plays well and sets up well, i don't see any reason not to keep it like that
