Is it possible that the touchups did not look "that" bad before the clear? Could the clear have spread the paint used for the touchups? Vid has mentioned that some paints change color under clear.
Not trying to defend poor work. He still should not have sent you the playfield in this condition. Maybe the clear could be sanded and leveled to some extent and you could salvage it? I feel really bad for you. I know I would be really torn up about it. Getting my money back would not be good enough. I think GAP should replace your playfield. Thats what I would do if I effed up someone's playfield.