That X-file thingy was just too funny... LMAO
I get the feeling that Ibanez's original intention was to come up with totally unique designs on a small production run for the domestic Japan market. The evolution of various models in the J-C line must somehow be driven by the Japan market. Lately we see the new J-customs fairly similar to the Prestige models, which may explain a certain convergence of design desired in Japan and US market (such as fingerboards, exotic tops, etc).
But as someone mentioned before, Ibanez seem to be more experimentative when it comes to J-Cs. All the additional cosmetic details and fancy electronics (Roland pickups, Piezo, etc) are not likely to be placed on mass production models unless it is market justified. So to me J-C really is like prototype cars which serves as R&D models or market tester. It is also why J-Cs always have that "exotic" flavor to it. I agree with the point that Prestige models are top-of-the-line production models, and their similarity to a few J-C models could very well be the result of success of a certain J-C design.
One thing we cannot ignore is that the J-C line does have a market in Japan on its own. Otherwise, major stores would not bother to carry them. Based on what I have seen and heard from guitar shops in Japan, J-Cs are catagorized as high-end over Prestige models. In terms of quality, by all means, this does not necessary mean Prestige is one notch below J-C, but pricewise J-Cs are in general more expensive than Prestige in Japan.