Amakusa Shiro has been in a lot of anime including Rurouni Kenshin (the later fillers though lol) and his real story is very interesting. If you know the story his actions in the anime make a loooot more sense. If you don't know, the tl;dr is that there was an enclave of Christians back when Christianity was banned in the Edo period and they took this young kid, Amakusa Shiro, to be the 2nd coming of Jesus. He took on that role and led the colony to an ultimate defeat after a long holdout against the shogun's army (supposedly they were betrayed by someone who defected from the colony), and Amakusa's head was displayed on a pike. The fact he looks like other characters is just recycling; it's the same reason Saber's model is used for half the other spirits lol. That part bugs me too though