i think it was a remnant of the affection points system
But they still use that, no..? The three irreligious options have different reactions and theres no moment where you can choose a route and it just depends on which characters you spend time with the most.
The bit with the religious beliefs is the one instance that changes anything and all it affects is getting Carlos' wet dream scene
You choose a route at the cabin class trip at the end of the first act
