I agree that they are painted on, or maybe just ‘enhanced’ but clearly not natural.
Actually, I saw a show on CBS about an anorexic woman (Isabelle Caro, posed for the super disturbing billboards at Milan fashion week 2007) where it was clear that she drew on/enhanced her freckles. When the interviewer asked her about it, she said it was to take attention away from her body. I don’t think that Amy W. is clinically anorexic, but she certainly has body issues (boob job notwithstanding) so I wonder if it is related. On the other hand I wouldn’t be surprised if she (and her makeup) was just sloppy drunk.