Religious liberty in a political context works only if the parties involved want peace. When the Turks attacked Vienna in 1683, both sides agreed on one thing:that the God of battles would decide the issue. Pretty much the same applied in the clash between the Christians and the Cathars. Feudalism is the name we give to the polity of the time, Europe was not a single entity except quite loosely something called Christendom, not a unite but more like 10,000 private estates of which maybe 1,000 were controlled by the bishops and monks. There was a spiritual allegiance to the pope and a broader allegiance to a hierarchy of overlords, the most important of which were called kings.
But in the colonies there was no such sharp divisions among the sects. Madison saw the matter in much the same light as he did when he treated special interests in his Federalist #10. That a majority faction is a danger to liberty but that a balance among them worked very well.
Yeah... heard all that before. rather a rosy description that downplays the role of pope and church. Not buying it.