Does savage shoot every rifle before it leaves the factory? could the wear on the bolt be from that? Maybe I'm not noticing it on the pictures, but it doesn't look like anything too crazy on the bolt (the rail, I'd be disappointed and a new rail shouldn't look like that). If you aren't happy and you feel like SFRC is screwing with you, return the rifle and just don't buy from SFRC.
Personally, I believe your expectations are a little high. A tiny bit of wear on a bolt, it happens, boxes get opened, actions get cycled, triggers get pulled, THEN people decide if they want to buy it or not, that's how it works in stores. As for the rail, I believe that is a result of a poor packing job int he box, but it being a "non-standard" box wouldn't bother me. Honestly, I just recycle the box anyway, so who cares whether it is factory or not, all that matter is if everything was ok. In your case, it looks like the rail suffered some cosmetic damage. I'm not sure what the margins are on guns, but getting 15% off, and expecting another 15% due to some marks on the rail seems a little steep to me. Maybe I'm wrong but I don't see this resolving itself in a way that makes you satisfied.
The world has changed, right or wrong, the client isn't always right anymore. I've given up on trying to convince companies I'm right, now if I am upset, I just take my money elsewhere.