Well chimaera, it's always been possible that the messing around on Earth of the Godmen and Leviathans may have been responsible for the species' creation in the first place.
First, there's the speculation about Six trying to stop Tchort from becoming something powerful in the future, such as a Leviathan.
Second, there's the Faceless, who are 'half man, half god, half rock' or whatever. They are growing in sophistication, and will probably become a powerful post-human race, such as the Godmen.
Third, there is the player, about whom there is all sorts of speculation. Did he train as an agent for Oculus to infiltrate the Faceless in the near future, and then go back in time to steal it and disappear afterwards (into the future)? Did Six or Tanner kidnap the player as a newborn to train them as a blank-slate slave to carry out tasks? There's the two 'coincidental' stories of the ferrymen. Is the player just a physical manifestation of psi energy, like the beetles?
So it wouldn't surprise me to see that divisions caused by time-space traveling into Earth may have created the Godmen / Leviathans. Perhaps they were one race previously, and got split at this juncture. I don't know enough, but perhaps it would be good to collate what was learned about these aliens in the expansion.