I wouldnt read too much into it. The main story was altered many times even right before release. Many things which could be key elements were deleted. The story is more of an excuse, inconsistencies are most likely just that rather than some extremely deep understanding od things. Each game they hint to more going on in the back and each game they dont develop it but hint at it again. At best you could say ds2 has the most human and direct approach to the issue, with the bonus content included obviously. The main explanations for why some things are in that universe completely opposite to how they are in real life is that the guy who wrote it just wanted it like that.