At this very moment, there is NO Free Knights storyline. The RG material transferred to Free Knights players, which made alot of them angry.
These are taken from the main website:
The Ark is much larger than the intro area portrays it to be.
The above images are odd. At first glance, the sunny image could look like a Fallout Earth; however, it does not have the rivers of poison (or toxic waste) present in other pictures. This suggests that both images are post-fallout.
The second image looks like West Enocia - because of how the satellite view could interpret the trees as all that green - during a sunrise. The trees are kind of hard to notice, though. Both pictures show Arks but the terrains are highly unique.
I'm pretty sure all humans died. Their DNA was stored and used to create Neo-Humans. That being said, Mother was all alone and went all GLaDOS for years and years - sciencing things up until she could make the Arkana and Neo-Humans.
Lastly, the RG and Free Knights both tried political bonding with the new races. This suggests a time in which they taught their language to the Elders/leaders (and probably only those).
Commanders don't have to be inside an Ark. They can be at their own homes throughout the continent. Just because the land beyond East Chromia is blocked out, that doesn't mean there isn't actually an entire land there full of Neo-Human communities. That land may also be full of resources and lack Narak and Free Knights presence. It may also hold the RG Ark.
As for the period of time between now, fallout, and the game's starting point, humans generally have a knack nowadays for making everything 1000 years later whenever SciFi and Fantasy Future are concerned.