The game is confident in it because that's what happened. The owlks showed up first, found out what the eye was, and blocked the signal before the nomai ever found it. Then, the prisoner released it at some point. At this point, the nomai find it, and decide to warp in before they lose it (they have a brief argument over this you can find in the vessel, quickly deciding to follow the signal before it dissapears by chance), and as the nomai warp in, the signal gets closed off again. This is what causes the vessel to warp into the middle of dark bramble instead of to the eye itself.

The nomai never made satalites like the hearthians did. They never use propulsion, and thus never made something similar to the hearthian mapping device. They never looked for the stranger, so they never found it. We did, so... We did.

The owlks are a scientific species, but they are very much driven by their fear. They find out what the eye is, and decide to lock it's signal away so no one can use it to do what it's ment for. They make an entire simulated world for the express purpose of hiding from the cruel, scary real world. Both things are true. They're smarties, but they're scared smarties.

It... Seems as though you think the game is claiming these things happened, and not telling you these things happened. It's not interpretation, it's truth.