First of all, I hope you can understand my English, I don’t use it since 2007 and it’s a bit rusty.
My theory is that the observers “born” on the beacons. September’s big introduction in the series is on “The Arrival” episode, waiting for the beacon, so it’s clear it has some big connection with him.
At the end of this chapter, Walter tells Peter that he had to protect the beacon for September, as if he knew it was important for him. And it is, as September says he can’t touch the beacon, while Mosley and the others can touch it perfectly. There has to be some special connection between September and that cylinder, kind of "genetic" thing, as he wants it activated and disappeared below ground, that is the mission of the beacon. Of course he can’t “intercede” as he can't touch it, but I think he intercedes after all. Walter says that he “felt” he had to hide the beacon. Probably this “feeling” was induced by September, as at the beginning of “Inner child”, where one of the workers is induced to find the child.
Finally the beacon buries itself and disappears. Nobody finds it. My theory is that it has travelled through time.
A few months later, as shown in “Inner Child”, an “observer” emerges from the underground, but he had been locked there more or less 70 years. Maybe he born from that beacon which travelled through time to the past?
I remember September saying to Walter in “The Arrival”: “it’s too much time to be without something you love”. Maybe some reference to the inner child and the beacon? That “long time” could have been the 70 years the Inner Child spent in the underground; maybe September met the child in the past.
When the inner child was found, he was on a kind of jail and probably he suffered experiments. One interesting detail of the room where he was is that it has a bunk. Maybe the experiments were done with more observers? Was September one of them? At the end of “Inner child” chapter, September and the inner child look each other a long time; they recognize each other?
To speculate a bit more, I think probably those experiments 70 years ago were made by Robert Bishop because in “The arrival” episode Walter buried the beacon on his grave. Maybe it’s a kind of clue or “joke”, pretending a relation between both of them. In front of the grave, Mosley says to Peter: "Shame you never met him”, so Mosley sure met Robert Bishop, and if it’s true and he is bald as the observers, maybe he is the result of experiments with observers and he is there to take the beacon for more experiment proposes, traveling to the past to give it to Robert Bishop. Probably NSA and CIA know that these experiments were made as they are very interested in the recovery of the beacon and the child, probably to make their own experiments with them (the agent that appears in “Inner Child” episode talks about experiments and the child looks at him, first with fear and later, at the end of the chapter, with distrust and kind of hate, so he knows it can happen to him again).
About the origin of the beacon; they were made by the first people? Something related to the vacuum machine? The design is quite similar.
The beacon is composed by iridium; this name of “iridium” comes from Iris, who, in mythology, is a messenger who established the relationships between gods and humanity. Maybe the observers are a link between the First People and us and they have been “activated” now that the incident of 1985 makes possible the construction of the vacuum. Iridium is a too much rare element to not be something “symbolic” here, and the two known beacons arrived after 1985.
Other symbolism I found is in the title of the “Inner Child” chapter. “Inner” meaning “child inside something”, maybe “Child inside the beacon”.