I'd say, that the inability of Elysium project to sustain itself for longer than a century - while much more complex terraforming machines of GAIA project stayed perfectly serviceable for literally millennia - is a big flaw in game lore.
Good point. There is some report in the game that says the alternatives to Zero Dawn are unviable but the reasons are in something like "appendix A" which we don't have. If I had to guess a reason, perhaps a self sustaining bunker would be large enough to be detected by the Faro plague.