In a semi-Christianized Japan, you'd have the Shinto-Buddhist old guard, and the Christian new guard. And the latter, once they have enough of a stable base, would divide between the ones who support keeping the original Catholicism and Spanish trade and the ones who support shifting into a more Anglican direction to break away from that. So the Reformation might reach there. Indeed, it already did IOTL, which is why the Tokugawas trusted the Dutch and English while expelling the Jesuits.
Basically, the clans would fight each other, supporting different causes and forming alliances under said causes to advance their own agendas, as IOTL. Look at the German princes who supported Luther to expel the monastic orders. A Japanese Christian state need not be Catholic.