I haven't thought about that... I doubt that the thing we see in the sky of the ocean biome is nothing, so I can see that it could be the colony ship.
Do you have any reasons other than it being a giant flying thing in the sky? Not that that's a bad reason considering it's the only flying thing in the sky, but it's not exactly conclusive either.
Although... It's only visible in the ocean biome. If it's the colony ship and they wanted to represent it in the simulation, why not put it on every sky? Why only the ocean biome specifically? Maybe an ocean planet is its destination?
I always figured that that ship over the ocean biome that we're talking about was a visual representation of the Master AI of the biome (Moeder) which is why the other biomes didn't have it.
Unrelated, but I think it's important. There was some talk earlier about whether the colony ship was heading away from (colonization) or towards (repopulation) Earth. I think it's heading away from Earth. The reasons why are that there were already Arks for repopulation. If the Arks failed at repopulation, it may be a safer bet to try to colonize somewhere else until a better method of removing corruption (or whatever causes the Arks to fail) is found that can save Earth, since the Arks were the best method of saving Earth at the time, as that was literally their purpose. The colony ship was therefore most likely not working as a long-distance Ark, but had an entirely different planet (or moon, or whatever celestial body they had in mind.) Or maybe it was never supposed to land and instead function as a safe research base of sorts.
So much for safe though.
And while we're on the topic... The unconfirmed launch at Arat Prime... Seems to be just that. Merely unconfirmed. Because no one stayed behind to confirm it to the Sanctuary, and there was no one in the Sanctuary that would be able to see the confirmation. I'd say it's a pretty safe bet that the colony ship is the launch being talked about in reference to Arat Prime, seeing as the only way to access the GenSim, which everyone on the colony ship was in, is at Arat Prime. Not to mention, due to the lockdown at AP, it might not have been possible to confirm a launch to the outside world.
In other words... False alarm. Everything's fine at Arat Prime. More or less.