If the experiencers are in reality, not a simulation, it can not mess with time prior to its creation.

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Extrapolate the various ways such could occur - add chaos theory/butterfly effect to stress point.

If simulation - ie can be turned off with no effect on said snake, remove above.

Many, many ideas could be postulated for your first two questions, and the third reminds of not only such things as the matrix, The magicians and a handful of others, but also A rather indirect and inefficient way of facing said difficulties.
Not to say it's not a possibility, but when you refer to something as virtually all knowing with the ability to traverse both space and time (and all the information available to such) it becomes something other then a program. Especially one limited by laws.

As for your last...possible because of the spreading of a certain book, hardcore adherence to it being the only/ultimate truth, mass persecution of those who disagreed and the continual "handing down" of said beliefs thru generations.

The sun revolves around the earth - and such was the truth under penalty of fire to disagree.

Tho I'm sure there's also many others who would not agree with less ribs - both in those who have read that story, and those who never have