I think repaint costs are quite reasonable for what you get, though the prices listed in the OP's link do seem a bit high. I had my bike painted by a professional one man shop for around $700, which included color bands on the seat tube, contrasting head tube, decals, and aligning the frame. Even at $1,000, you're way below the cost of a new custom frame. The only way you could beat that would be to buy something like a new Soma frame, but then it wouldn't be custom and you wouldn't get any color choice.

Of course it doesn't make sense for beater bikes or flipper bikes, but then this is the C&V forum, not the flipper forum.