Maybe this was the start of the end when the Gauna destroyed the world and humanity had to flee using the ships. It's fucked up but sometimes I wonder if Blame! (the very first manga) isn't the last part of the chronology in Tsutumo's work.
Sidonia and Aposimz are related and part of the same universe, showing the creation of the Megastructure, synthetic humans (by using placenta) and the gravitational beam emitter ( which is absolutely huge in Knights, needing several battle ships to transport it; but has the size of a pistol in Blame!).
Biomega seems to be another universe although it depicts the Toha Heavy Industries in it too.
If this theory is right, the chronology would be: Abara, Knights of Sidonia, Aposimz (probably many years/centuries after the end of Kinghts), Noise! and Blame!
There are a ton of wholes in this theory tho and probably Nihei only like to "borrow" these things from one manga to the other.