I've successfully indented chainstays to increase tire clearance. I fabricated a die out of a short round piece of bar stock about 3/8" diameter brazed to a plate, and semi-circular cut in a block of plastic for the outside of the chainstay, and used a 3" narrow-jaw vice to press the die into the inside of the chainstays, covering both with small pieces of leather to keep from marring the paint. It worked beautifully. Added a good 5 mm more clearance on each side.
This won't increase the stiffness, and may require some cold-setting to realign the rear triangle afterwards. It's easier with high-ten chainstays.