[spoiler]About the whole new civilization thing, I think it was meant to represent a new fledgling species that the forerunners and flood did not yet know about, but was tragically snuffed out before their time by Halo. That civilization is dead, it stopped transmitting after the Halo wave hit them, and as they were previously undiscovered, there was no way they could be reseeded, so they can't be the owners of the ship that landed on Alpha Halo. I think you're over-thinking them, and they were there simply to underscore the tragedy of the Halo's firing[/spoiler]