I explained in Bowex chat already this probably is the case. The emperor worked more as a figurehead, a legitimization for the reign of the Shogun and his Vassals, the local Gouverners (See lord Hakkeera). After the nomad war kusari essentially seems to have been restructurated, to more resemble Japan during the Meiji-Period, with the emperor having actual power over Kusari. Samura also probably never instated an Emperor, it most likely installed a Shogun instead of the former one (the actual reason for the dragons wanting to install a Shogun rather than an emperor).