I've contacted him about these issues and his approach is that guitars will get scratched anyway and it's sound/playability that counts and this damage can happen when setting up. Personally I don't think this attitude is right and if I'm paying a specialist to carry out work on something, I expect to get it back in the same condition I sent it in (especially as it's effectively a brand new guitar).
All that matters is what you the customer think. He of course is entitled to his opinion but ultimately it's your guitar and after he's done working on it, you have to happy with the results.
Something else I'm struggling to get my head around is he replaced a shim under the nut to lower it and it seems the new shim was too wide for the nut pocket. Rather than order the right size shim or file it down, he cut the nut pocket wider to fit the shim.
That just seems like he was being lazy in a way but I would ask him point blank why he did that. After he tells you, I'd be interested to hear what he said.
The point of the post is to get some opinions on whether this is the norm when having setups done by Luthiers, in which case am I being too picky?
Guitars will also get tiny little scratches from being handled and played but the ones in your pics aren't those types of scratches, especially the ones on the headstock. As another poster pointed out, those scratches appear to be the result of using the wrong tool for the job which indicates sloppy, careless work.
He's offered to try and polish out the scratches but I know enough about paint/clearcoat correction to know it's not a quick job and I'm reluctant to send it back in case it ends up in even worse condition.
Go with your gut. If he screwed it up once there's a chance he'll screw it up again. If it were me, I'd cut my losses.
I had one local tech work on a guitar for me and while I didn't have issues like yours, I didn't like the way he did things so I found another tech who I am happy with. I also make it point to meet the tech who's going to work on my guitars in-person so I can establish a relationship with them. I want them to know that there's a person attached to that instrument and both the player and guitar need to be treated with respect.