Then why is there a timeline where Lavos doesn't fall?
When you play CT and defeat Lavos (New game +) before helping Ayla freeing the Labura Village's people from Azala, you have an ending with the begining scene but everyone is reptites...
So My guess is that Ayla went to fight Azala alone, but failed. So Azala sent the reptites on a rampage over Ayla's village (forgot the name : Ioka?) while they were rampaging Lavos fell from the sky destroyed tyrano Lair but some reptites survived.
What is still wierd is the fact that Azala knew the coming of Lavos, maybe it was all part of his plan to kill Ayla and raid Ioka(?), but Crono and co. went and killed all hope for reptites.
I agree, Humans were loosing when lavos fell.
Azala would never have summoned Lavos (I mean if Magus couldn't who could?) and has stated in CT Lavos is a parasite, using earth (or CT planet name) energy by corrupting the planet, to finally reproduce (in 1999 AD) so other Lavos could go and leech some other planets energy.
I think too that Lavos was here by "luck" he could have missed the earth to end up in the sun and die, that's the risk of life (I hope you understood me on this)