The aftermarket modifications that can be made for any handgun are limited primarily by the imagniation and wallet of the owner. A handgun manufacturer, however, must deliver to market a product meeting specifications approved by the applicable governing authorities.
Smith & Wesson and some other major manufacturers are able to afford the luxury of "custom shops," but I would think that factory customization for limited production pistols such as the Rohrbaugh line would be, at this time, a "bridge too far." It is easy to ask, "Why not?", but it is a bit more difficult to determine, "How and when?" -- especially when one is tasked with finding and arranging the financing for such elegance.
I respectfully suggest that we have in the Rohrbaugh line of handguns the finest pocket pistols yet designed and marketed. The Brothers Rohrbaugh have devoted their lives and fortunes for the past decade and more to bringing these masterpieces to market.
But to anwer more specifically the question originally posed, it is my understanding that all quality refinishers, in order to maintain their own reputations for quality work, would want to "prep" a gun before applying their particular magic to it. Personally, if I were running a refinishing operation, I would give a gun that was apparently "naked" the same treatment I would give one that was already anodized or plated. I would make certain that it was stripped down to its bare metal before I applied my own proprietary refinishing. The cost of doing so would be the same, I believe, whether the gun were anodized, plated, or simply "naked." After all, it would have been handled many times before reaching my shop and would probably have who knows what types of oil or lubrication on its surface. The "prep" costs, I would predict, would be essentially the same in all cases.
(All right, you engineers, chemists, and metallurgists out there, here is your chance to refute this lowly attorney.)