Based on the uneven pin striping on my bike (both the thickness and the distance to other paint detail) I would think at least some CVO models are done by hand.
Sadly, bad quality doesn't qualify as custom either. If it did there are a whole lot of us who could claim true custom status.
For instance, a bunch of us from 2005/2006 had the next best thing to signed parts; finger prints of the folks who handled the parts at the paint vendor, under or in the clearcoat, no extra charge.
As I mentioned, Harley claimed that a couple (few?) models had hand painted pin stripes. I'm guessing yours is one of those models. After seeing the results, do you still think it was a great selling point? Btw, you can get the same sort of thing on pretty much any car dealers lot these days, "custom" tape or paint stripes applied as you wait. Doesn't make the car or the paint job a true custom. Just sayin'.
Jerry