That's interesting. Though as Tamamo-no-Bae pointed out, that begs the question about what Kotarou was doing on the Moon with Kagari while she ran these simulations.
If it's like you said, then the first incarnation of the world worked like this:
1: The earth goes through a natural coming into existence without any meddling of Moon Kagari's theories, as she does not exist yet.
2: The earth lives out its course, and it naturally reaches the point where salvation is needed.
3: Salvation occurs, wiping out humanity. This also, like you said, sends up enough aura onto the moon to form Moon Kagari.
4: Using the previous history as her basis, Moon Kagari forms her theory
5: Since Kotarou existed in the first history, he has her ribbon in his arm. This is a strong enough bond between the two to let him appear on the Moon.
6: Kashima Sakura also existed in the first history, and her hatred of humanity was so strong it also allowed her to manifest things on the moon (in this case familiars.)
7: During all this, no new histories happen on the actual Earth. Moon Kagari is just using her theory of life to run simulations that'll help her decide what she should do with the Earth's aura.
Wow this is all really complicated. I think Tamamo-no-Bae's third theory is so much easier to understand, whew.
Though I think Tamamo-no-Bae's third theory had a bit more support from the visual novel in terms of the whole "worlds or simulations thing." In the Moon Route, when Kotarou talks about/reads the theory of life, he refers to the branches as "Branch worlds." This makes it sound more like the Earth just repeated salvation endlessly until the theory was completed. As opposed to being simulations of that.
Furthermore, if none of the heroine routes happened and they were all just simulations, how would Kotarou have memories of the simulations? He did read the theory of life a bit during Moon, but he had memories of his previous lives even before that. At the beginning of the Moon Route, he says its like he lived the same life over and over, because he has memories of different lives (one where he married Kotori, and one where he married a businesswoman, for example.) If those lives were simulations, and the numbered list I gave above were true, then there's no way Kotarou could remember them. He didn't experience them because they weren't real, so there was nothing to remember... right?
But my memory of the exact lines is a little hazy. Perhaps you are right and different lines in the visual novel prove it, and I'm just not remembering them.