That scratch a tough one to argue fault. It can be a scrape from a prior HG replacement, engine rebuild, or any sort of rough-handling of the block by the shop, or yourself.
Last time I had something machined (albeit heads), 0.005" was considered a minimum cut. I think I would try to use that figure to calculate piston clearance height and resulting CR (also see about available HG thicknesses). If acceptable, I'd prefer to have it machined. You're far enough in it seems dumb to cut corners.
I am sure I did not do the damage but I agree that it would be something that would be hard get them to fix. There is a similar scratch on the other side that touches the new sleeve they put in, I am not very concerned about that one because It is so minor and you can't feel it with your nail but you can see it. They also scraped the **** out of some other sides of the block.
I know I should just take it to the machine shop but I don't want to deal with them again and the only other one that I know is good Is expensive and far away. I am curious on the JB weld idea though, I heard from someone that if it's done right can hold up just fine. I also read on a forum about taking a punch and building material up around the fire ring. Are any of those things anyone has had experience with? Or anyone else with any good bad ideas?