So, I've been thinking about some of the different timelines, such as the Keystone, the Reptite Dimension, etc., along with some comments in Chrono Cross. Would it be safe to assume that there are infinite parallels of each universe? For example;
In the Reptite Dimension, Lavos never appears and the Reptites conquer the Apes. However, would it not be safe to assume there is another dimension in which the opposite occurs, and the Apes conquer the Reptites (And Lavos never falls to the Earth)? While it's never used in the storyline, it's always a possibly dimension that was never created (Or seen).
It's drawn from the show Sliders (If any of you remember it); basically, it theorizes that there are relatively infinite parallel Earths, in which each has an alternate outcome of possible events. So, a parallel of each world in Chrono Trigger would exist, where in variant A Crono is never born, in variant B Marle is never born, variant C Crono is killed as a child, etc. This doesn't have many applications, but it could still serve to explain the existence of the Reptite Dimension.
Another possibility of the Reptite Dimension is that the Reptites managed to defeat the Apes nonetheless. They were known to be far more intelligent than the Apes to begin with, and it is entirely possible that an alternate version of the world exists where the Reptites were victorious. This would also help to explain the "perilious times" that is infered in the Reptite Dimension Chronology; since Lavos still fell to the Earth, he would awaken and destroy it whether the Apes or Reptites were victorious. In fact, it could have delayed it; though unlikely, it is possible that when the Enlightened Ones syphoned Lavos' energy through the Mammon Machine, as well as disturbed him directly through the Black Omen, it altered his progress in absorbing the Earth. I can't substantiate any of this, but is in fact a possibility.