If these imperfections were on a $2,500 hand fitted custom gun, I would be outraged. If they were on a $600 mass produced gun then I would be indifferent. The scratch by the safety could indicate there is some sort of a raised burr on the safety that is scratching the polycoat.
This isn't my gun though, this is your gun. If these things bother you then you can call CZ USA and they can make it right. There will be an inconvienvence of shipping the gun back to them, and being without it for a time, but I would expect them to handle at least the frame scratch if not the other issues as well.