For the game's purposes, "religion" is really just a set of beliefs that are used to endorse political legitimacy. Looking at things this way, Confucianism works well as a religion - it means that locals see adherence to the Confucian philosophy as being the thing that supports one's claims to legitimate rulership. The distinction between Confucianism and Buddhism can be clarified as a Buddhist state/province relies on state patronage of Buddhism (i.e. through supporting monasteries) as a source of legitimacy.
To respond to an earlier question, Nestorianism and Manicheanism died out in China during the Tang period because of official persecution. Nestorianism returned with the Mongols (as did Catholicism, actually), but disappeared in the early days of the Ming.