MOST luthiers you find at just any guitar shops will pretty much just scallop out the same amount of wood all the way down the neck. When I do it myself, it allows me to control exactly how deep each is. The first fret for example, isn't very deep at all, but up at 24... yeah, its pretty deep.
As for changing your sound, in my experience it will (its a more noticable change on say, strats though). But its a very sbutle difference. And generally can only be heard without very much distortion. I dont' think I've ever heard someone say that it sounded WORSE, just different.
