The opening/religious setting is basically 1:1 DOS2 - your ship is attacked, you drown/fall to death and some god seems to intervene and save you. Then you have a religious cult that is trying to take over/save the world.
Reusing that opening and setting is not necessarily bad, but a little bit lazy.
Agree, also if you go one step further back you start out on imprisoned on the ship with an attached/inserted foreign object/lifeform that you need to get rid of. I was a little taken aback on my first playthrough and unfortunately I wonder if it was more a case of it being a deliberate choice to be cute rather than unintentional laziness.