That's probably not the intended case at all. Federer is using the vapor 4 with a custom made outsole, probably for better traction/speed in combination with the benefits of the original shoe. When you're the top ranked player, why not have the best of Nike shoes all molded into one? It's not a paintjob or a design to trick the public into buying something else.
But who knows what's actually inside the shoe? What type of cushioning system? Support system? If the cushioning has been taken out (like some pros like)? It could basically be a totally custom made shoe that just has uppers that look like the latest model. Suffice to say that it's not an off-the-shelf shoe. So for people that buy the shoe because they want to wear the exact same shoe as Federer, they are out of luck, and are fooled into thinking that they are buying the exact same shoe that Federer wears. So, to me, it is a "paintjob". Just like paintjob racquets fool people into buying a racquet they think a pro uses, but it's actually not.