Ok, I love how you've tied it all together. I do disagree with you on this point though...
"I believe the "termination" the overseer does is what happened to the city of Nosti on Scorched Earth, and what nearly happened to the tek village on Aberration. I believe it does this because it doesn't want people to expose the ARK for what it really is."
... because it makes no sense. It wasn't the size of the tribe, or the intent of the tribe, as both tribes were very different in both respects. I think it has to do with civilization, as a whole, which slows down and in some cases even stops, evolution. Which I think is the entire point of the ARK, to force evolutionary growth. The Homo Deus are trying to create MORE Homo Deus but the only way they can is by forcing certain humans to evolve. Those with the right abilities, the right genetic qualities, ascend. All of this as a way of saving the endangered Homo Deus.
The One Who Waits is either one of a scant few Homo Deus or the LAST Homo Deus. And the reason it is contacting you is because something has changed between the creation of the ARK and now. I posit that, possibly, the Homo Deus were more numerous when they created the ARK, but as time went on they grew fewer and fewer. This caused the equation that ran the ARK to change, pushing the goal posts further down the line as more information was needed to fill the void left by the Homo Deus who disappeared. IF the problem is the extinction of the Deus then it stands to reason that as they grew fewer and fewer the amount of evolution they required of the ARK grew exponentially until, as the last one OWW determines the equation is now unbalance-able by means of the ARK.
And so it must be solved in another fashion, enter the broken ARK and teleporter to earth directly. Does that gel with the rest of your theory?