mother sphere initiated the war, but organic humanity was at fault
naytibas weren't a reaction to mother sphere, but the catalyst
the research labs were already long established and overstepping their boundaries
even if humanity was self destructive, they would have been easily corralled by andro eidos, while naytibas have inherent and uncontrollable destructive instincts as well as the corruption ruining the environment
andro eidos continue to be created in the image of humanity because mother sphere wants to continue their legacy, else she would have visually changed their form
raphael marks never preserved humanity, but knew that mother sphere's andro eidos did so better than naytibas, and sided with xion instead of fixing his naytibas
raphael marks has always withheld information