On one hand, we have exactly what you described: "Uh, we invented some synthetics to destroy you every 50,000 years to keep you from getting destroyed by other synthetics. You're welcome?"
And on the other: "Oh what's up humanity, we need your help to stop this theoretical sub-atomic particle from fucking your shit up... Sooooooo, we're just gonna go ahead and harvest the shit out of you for your own good. Kthnxbye."
Either way, the events of the game are still moot since they don't add anything to either resolution.