Thank you for your comment.
I thought of this, I just forgot it to write it down over there.

At first, the GTVA searched for many places in their worlds where the survivors from the battle of Capella can live. Actually some of them find a place they could call home. But many others don't. And there is the system Barnard's star which is very imprecise explored. And so, the GTVA thought they get a place for all of the survivors of the destruction of the Capella star.
Then, the GTVA finds the remains of the Hammer of Light. Actually the attack the remaining troops of the "HoL". But the last finish stroke will be arranged by Atapeth and his rebellion. And this rebellion also attacks some ships and the outpost in the system and destroyed most of them. Actually there is a bloody war, because they want to get Atapeth. Like in the FS 2 Main campaign with Bosch.
But you are right, often the player is asking: Where does this ship come from? I hope I can answer that question with this explanation. Please give me more Feedback. Thank you very much!