If you mean you tell them what you want on it, and they make it for you... no, I don't think so, and if they did, it'd probably be too expensive. What exactly are you looking for in a motherboard that you can't find in an existing one?
Well not to mention that kinda goes against the foundations for the two companies: both Intel and AMD boards are designed for stability ... the point of a customized board generally is to add overclocking features and additional connectivity options etc. Overclocking isnt supported by either company and features are controlled by the chipsets.