How do non-factory routs affect tone?

Wood is a collection of more or less parallel fibers, running lengthwise
through the body. Wood has very little strength or conduction 'sideways'
across the grain fibers. That's why the grain fibers have to run
lengthwise on the neck, for example.

Where the fibers are cut, like for the pickup routing, this 'straight
grain' bundle of fibers is cut. This obviously doesn't prevent a
solid body guitar from soundin good, but my point is that once there is ANY
routing for the the neck and pickups, it doesn't seem to make much
difference structurally. Especially if it's not routed any deeper than
the routing for the neck, which has effectively cut-off any
straight-grain to the bridge area anyway.

Most solidbody guitars aren't very solid in the area between the neck
and bridge to start with. Even the solid-maple center-section on 335's
is fully cut-out between the pickups. I purposely use oversize routing on
some of my solid body guitars, not just to allow humbuckers, but to
reduce the weight and increase the resonance on guitars that would
otherwise be fairly dense, bright, and heavy.

When we 'repair' any extra routing, we're simply filling-in some of the
extra empty space. Adding or re-filling extra routing makes little
difference in the strength, and the difference in tone is usually not
much different than a similar guitar made from a lighter piece of
wood. Each would have a lower resonant frequency and a bit less
'solidbody' upper midrange emphasis.

In my experience, oversize/extra routing can change the weight,
resonance and tone, but that's not necessarily a bad thing. And with
the current craze for high prices for ultralight guitars, it could be
very a good thing.

On Fender guitars, especially Strats, extra routing usually affects the
price more than anything else. I've added, and repaired extra routs on
these types of guitars for customers, but I think of this largely as a
cosmetic issue. The tone doesn't change much more than the weight of
the wood added or removed.

Quite a few otherwise desirable vintage guitars are routed for non-standard
pickups and customized control cavities, and these instruments can frequently be bought well below the price of their unaltered cousins. I've been told that a rout for a middle pickup in a Tele, for example, can actually increase sustain, and I've noted that Fender actually heavily routed Teles for a time when lightweight ash was in short supply in the 70's.