Actually it might be complicated. As we can read in vanillia Blood Dragons' description, they fight for "restoration of their Imperial line". This could mean that both Emperor and Shogun are present in the government, with predominant role of the Shogun. Like in Edo Period of Japan, under Tokugawa Bakufu.
Figure of Emperor could be just symbolic, like in very turbulent times from Onin War till the Meiji Restoration.
