Except for the ship and the invulnerability regime, it did not change. This mistake appeared when 3 times the Order refused to fly to the black hole (I think so)
because after that all dialogues and characters of the bar in Omega 3 and the ability to choose objects on the map disappeared and only the requirement to fly to the black hole jumped in (that's when the idea to add your own ship arose).
Now the whole senarium is in turmoil. So the changes here are absolutely nothing.