They do have a custom shop, Guitar Universe in japan has a few custom models that you can order from them. One of them is a yellow (lemon drop) flametop Love Rock which is really nice. It has a satin finish that looks great (http://www.cyborg.ne.jp/~universe/tokai_order10/ltduf5175/lsltd_uf5175.html). I've also seen a PRS Santana replica for sale in japan (without Tokai logo), it was built for a music store in japan (the price is $3500 + shipping!). I don't know if it's possible to place an order for a custom built instrument though.
Mike