It's not impossible from a scientific perspective for a planet to be terraformed and seeded with intelligent life by some overly advanced spices (you can say "god-like"). Or to create a simulation with intelligent life in it and to save some resources by starting 6000 years ago from a complex seed state rather than simulating 16 billion years of physics to see the intelligent life emerge or not. That would be rather inconvenient for the PhD studying simulated intelligent life, he'd better just purchase and rearrange some pre-computed data.
The difference between science and religion doesn't lie in disagreement over particular facts or any facts at all, the difference is in the approach. Religion can explain anything but predicts very little (except for sociological phenomena which it predicts rather well). Science is built around making verifiable predictions but doesn't in fact give any answers, only theories that are (mostly) consistent with observable events (so far). They can however agree or disagree over any particular set of facts. Take any religious belief and you can build a scientific world where it is true.
The difference between science and religion doesn't lie in disagreement over particular facts or any facts at all, the difference is in the approach. Religion can explain anything but predicts very little (except for sociological phenomena which it predicts rather well). Science is built around making verifiable predictions but doesn't in fact give any answers, only theories that are (mostly) consistent with observable events (so far). They can however agree or disagree over any particular set of facts. Take any religious belief and you can build a scientific world where it is true.