My instinct is that the separation between science and religion comes about from a fundamental difference in method in approaching the truth.
Science is concerned with the truth of categories. It assumes that there is no such thing as a fundamental change — creation ex nihilo — because such an event would be beyond all conception in categories and quantities. In terms of time, the scientific method is always concerned with the past and the future: the outcomes of perfectly repeatable situations in the past leading to future predictions.
Spiritual experience on the other hand is largely concerned with the truth of Presence, which is manifested in precisely the transcendentally unconceptualizable novelty happening now.
See e.g. Isaiah 43:18–19:
Do not remember the former things,
Or consider the things of old.
I am about to do a new thing;
Now it springs forth, do you not perceive it?