I have, although not for a bigger barrel. There's not a lot of material to remove before you get the exposed foam. I'm not sure if it's waterproof or not but I used clear coat to seal it to make sure water wouldn't soak in. Ultimately I full length bedded my Kimber MT like how my Fieldcraft is, and it turned into a sweet little rifle after that.
Can't speak to rigidity from a manufacturer perspective with enlarge barrel channel, but I've seen some with carbon barrels online in factory stocks so I know it's been done. Good luck with your project. Update us if you try it!