I still have no idea where the ecosystem was even meant to have come from. The ooze doesn't create organic matter, it just rewrites/mutates it. I have a feeling the writers assumed it did.
Still don't understand how Elden got changed, either. There are contradictory references to exactly what a 'construct' is and it's not at all clear they aren't one and the same as synthetics. They even call those crash dummy-like things 'constructs', which were clearly machines and Elden says, "I'm not the dumb robot anymore."
As for the mountain, that was severely anti-climactic. They just hand-waved a big mystery in front of the reader and never bothered to explain it. Even the signal, of apparent human origin, just seemed to be put in there for the heck of it.