Yeah, I thought about the ending some more, and the more I do, the more I like it.
The first question that the article you linked to asked is only half-legit. Its a paradox that the show addresses in season 2. As soon as time travel that influences the travelers happens (snap) you can't tell the genesis of anything: ideas, cause and effect, nada. There is no beginning or end to the infinite, and the same applies to an infinte time loop. Similarly, each alternate reality is dependant upon the other to exist. Not only is Jonas doinking his Aunt, but he is his own Great-Grandfather...and Martha is her own Grandmother. In order to exist, they must have all sprung into existance at once. Sic Mundus Creatus Est.
I think its pretty clear now, since the Martha that goes to the origin world can remember Jonas in her closet heavily implies these actions are ALSO a part of a loop. This has happened before (not as many times as all of the other events we've watched over the past 3 seasons, but still an infinite loop). Afterall, if this only happens once, the Tannhaus family is rescued from a car crash by two dream people. That doesn't really make sense. That crash HAS to have happened at some point in order for it to be, eventually, prevented. There are loops upon loops. An inner loop that we viewed in the first 27 episodes, and an outer loop that brings the inner loop in and out of existance as the Tannhaus's either crash, or are eventually saved by Jonas/Martha. ...it just requires one more jump back in time in the origin world. It was suspicious that Tannhaus describes his family's death as being "run off the road." Although it wouldn't require someone to go back and actively kill them to restart Adam/Eve worlds, merely going back in time at all would do it. Jonas and Martha wouldn't exist to save them, and thus they are created again.
I've also been thinking about something the show didn't really flesh out. Ok, so there are two different Marthas and Jonases depending upon if she goes into the house to save Jonas before the apocalypse, or if she listens to Bartoz and instead goes with him and eventually her brother to become Eve. But, that means there are two Bartozes, right? One that convinced Martha and one that didn't. It applies to everyone! There should be two universes after that divergence. What was the other one up to? Also, the Adam that convinces Jonas to go to the origin world was from the other side of the "Schodinger's Box" world. The alternate reality where Adam murders Martha twice. He then goes back in time and convinces that other reality, the other box, to end the loop. That's weird.