The Protestant and Reformed faiths were not homogenization like Catholic. The different branches would either respect or despise each other. Therefore I recommend as a feature for the Rule Britannia DLC that the system used for the Islamic Schools be transferred to the Reformation Christian faiths (except maybe Anglicanism, but I'm an unwashed Catholic who knows little about the Church of England so my Anglican friends can correct me if I'm wrong down below.) You could have courts inviting thinkers and reformers form other denominations to gain their bonuses and the different branches could form alliances. For example you could have the Lutherans and the Zwinglists getting together to because they both hate the Calvinists. I would also allow both the Reformed and Protestants subsets to interact across the divide. You could have the Lutherans and Dutch Reformed getting together to appose the Anabaptist. Finally If a nation created a state church they could customize their own branch that would be called either "The Church of ___" for Protestants or "_____ Reformed" for Reformed.