Earlier quoted context omitted.
This is a case of “Whig History” that refuses to die
The scientific method didn’t exist before the Enlightenment. We had tolerant societies before the present. But the notion that science should trump religion is modern. That doesn’t imply a glorious present. Just a qualitatively different one from any period before the modern era.
Not particularly: in both the Medieval and Islamic worlds, the writings of Ibn Rushd (Averroes) introduced this concept. And, then as now, it depended on an irrationalism about religion (or a view that religion was a sort of noble lie for controlling the masses) that was widely rejected by the medievals who tended to prefer a harmony model of natural reason and revelation.