Engie referred to subject 7 as the super, and Snippy mentioned the GD tried to either find or make God, and had succeeded. What if Snippy IS the result of this experiment A man with the time-space-universe bending abilities of a god, but the mind and soul of an ordinary man. Snippy himself might not realize it. On that note, Zee Captein could be a very literal and physical creation of Snippy's mind, so could pilot and the rest. Snippy might literally be a god-like being, mad from loneliness, subconsciously creating company for himself.
Perhaps the 10,000 year old anomaly is Snippy himself. (put THAT in yer mug and drink it!)