There's also another random line from an NPC in the Crystarium's library that mentions Omega (without giving away its name) and the alien civilization that made it. Considering that Omega got to the Source after the Sundering, it could be possible that the people of the First somehow made contact with said civilization too (or with someone/something else that knew of its existence). Unless they got that information from the Crystal Tower itself, but why would the Exarch allow them to have access to such material and learn about the Source when he has been trying so hard to hide it (not even allowing people to get in the spire)?

And let's not forget about that bit about Omega being capable of cross-dimensional travel, as it's mentioned too during The Twinning. So I wouldn't be surprised if the Nier raid is related with whoever made it. Maybe something else followed uncle Middy and Omega, but got to the wrong shard?

Anyway, the dwarve's route seem to be the most feasible one, considering how they left it kinda unfinished in the side quest. Whatever waits inside, and whoever made it, who knows.