Well, there's no real point trying to explain why something seems awkward to me personally. But I think it's the blurring of the lines between story and metagame with the updates to the ship stats to coincide with the story.
I don't know. The whole thing just sounds like Dralth'a'gar showing up to destroy the World of Warcraft in expansion pack 17. Gaming as a service feels too corporate sometimes. It's similar to the subtle annoyance of how instanced encounters make the universe seem less real.
I also mentioned that "flipping a switch to enable aliens" makes the previous searching for alien life seem kind of pointless since the bits weren't there at the time. Unless they've been there for quite a while, which would be cool.
If I actually fired up the game and got into it again then maybe I'd feel different. Suspension of disbelief is a tricky thing. This isn't helping though.