It seems the effects of those crises are influenced by your choice of answer during its first narrative event. I don’t find the plague crisis to have impact either way, but for the religious crisis if you choose the answer that’s something like “all religions must be tolerated”, then the punishment is the opposite - you’re penalized in settlements that do follow your religion. I always choose this option given the AI’s missionary spam (yes, they still spam them - we just don’t care or notice as much anymore because of how inconsequential religion is), and this crisis has been an absolute breeze every time.