That is scary and disappointing to say the least. I believe all four color schemes use the same flame graphic dimensions. I can not imagine that they are not using a template that should be the same across all of the bikes. Mine has much better symmetry on the back fender. It likely all comes down to the experience of the painter. Just like all professions there will be a range from worthless to outstanding. I have read other posts of others having paint issues in previous years too, but I wonder if the recent recall regarding the hydraulic clutch ended up causing an unusual rush or something. The timing of the recall was close to the release for this year's CVO models.
That rear fender would bother me too, and the front fender paint run is not acceptable either in my opinion. Technically I am not sure if the dealer/moco has to fix it since you probably signed something similar as I did stating it was acceptable. I would think they probably will fix it though from what others have said.
As far as a scratch here and there (unless it is too deep to polish out easily) I think since you took it home already you should just fix it. I had to polish all of the upper surfaces of my bike. There were a lot of minor surface scratches that really show up on the dark blue (ultra violet blue) on my bike. I used a dual action buffer and polish and in a couple of hours it was gone and I was happy. Of course I had to wax after the polishing.
Anyway, you and a couple of others are starting to make me feel very fortunate as far as the paint. I wish you the best at getting it resolved.