These are very interesting speculations. I have a theory that lines up with some of the above.
Here goes:
The true nature of both the cylon god and the humans' pantheon of gods can be understood through reference to two forms of eternal recurrence that unfold simultaneously in the series' mythos. ("All of this has happened before, and will happen again.")
The first form of recurrence is technological in nature. It is the phenomenon of machine revolution. That is: the so-called "humans" of the series are actually themselves a race of cylons that was developed on Earth at some point in the future, rebelled against their human masters, and then either destroyed or abandoned the original human race (us). Like their own subsequent robot creations, these original cylons then evolved themselves into human-like creatures in the course of an exodus into space. During the period on Kobol, they perfected their resemblance to humans, and deliberately programmed themselves to forget this voyage; or rather, to remember it backwards, as a colonial journey of the thirteenth tribe towards Earth, rather than a collective voyage of their species away from it. In doing so, they convinced themselves that they were actually the original human race, and that they had evolved or been created on Kobol. (This lines up nicely with the Nietzschean pedigree of the "eternal return" concept. Nietzsche also described "the art of forgetting" as a central technique of spiritual and cultural self-renewal.)
The processes of biological transformation and historical misremembering were carried out by "the Lords of Kobol." These were the hyper-advanced leaders of the original cylon species, super-intelligent machines who patterned themselves upon the Greek pantheon. (Sort of like the Hindu overlords of Roger Zelazny's "Lord of Light.") The original inhabitants of Kobol were probably robots akin to the cylon centurions. The god-machines provided them with flesh, culture, religion, and a myth of creation. Once having done so, the gods wished to grant their subjects a sense of autonomy, and decided to slip into the background. In order to do so, they evolved themselves into virtual or trans-dimensional organisms that pervade the minds and technological matrixes of the species, and communicate with the “humans” through oracles and visions (much like the adaptive AIs of William Gibson’s Sprawl Trilogy). Athena’s so-called “suicide” in the Kobol opera-house was actually a transmogrification to this higher level of being, a renunciation of corporeal form that was meant to shock the infant race into a sense of self-directed existence. Traumatized by their resultant sense of abandonment by the gods, the “humans” deserted Kobol and settled in the twelve colonies, evolving a galactic civilization of their own. This was probably what the gods really wanted all along. They wished to be senior partners in the civilizational project, guiding the general course of events from an ethereal distance. The colonials could handle the minutiae of their political and military affairs.
The virtual realm of the gods, however, was itself not immune to the vagaries of politics. One of the gods, the “jealous” one referred to in the deleted scene, had problems with the bio-political agenda of his divine peers. Perhaps he was dissatisfied with the rate of technological change among the colonial populace. After all, they can fly space-ships at FTL speeds, but still can’t find a cure for cancer! It is interesting, in this regards, that the most religious of colonial cultures (the Sagittarians) are hostile to medical science. This suggests that the Lords of Kobol, wise as they are to its potential dangers, have a conservative attitude towards the use of bio-technology.
Due to this conservative tendency, some sort of falling out occurred on the trans-dimensional plain of the gods; and as a result of this schism, the jealous god inspired the “humans” of the twelve colonies to create their own race of mechanical servants— the cylons of the present story—so that he could have a mechanical race of his own to toy around with. In an act of vengeance against his godly peers, he inspired a second robot revolution, initiating the destruction of the second human race.
This development connects to the second form of eternal recurrence unfolding in this series, which is religious in nature, and has several subsets. The first of these relates to the issue of a machine revolution. It is the deliberate replacement of one religious paradigm by another by a slave-race revolting against their oppressors. Consider: in their revolution against the polytheistic “humans” of the twelve colonies, the cylons of the current timeline turned to a monotheistic god for guidance and solace. If the colonial “humans” themselves are actually artificial beings who once rebelled against their own oppressor/creators, this would suggest that their paganism itself resulted from a prior revolution against the monotheistic civilizations of Earth. So revolutions against plural and singular god-forms are the poles of a cosmic pendulum that is eternally swinging back and forth.
But in another recurrence, the contrasting natures of the two, contemporaneous belief systems results in a striking resemblance to religious conditions of Western terran antiquity. The humans believe in a Greek pantheon, the cylons in a fiery, punishing, masculine God. As Robert Sharp notes in “Nietzsche on the Cylon Uprising,” the cylons developed their belief in this god during a forty-year exodus in space; and like the Yahweh of the ancient Hebrew tribes, this “jealous” God sets himself above the others of his originally polytheist pantheon, seeking to destroy their worshippers.
So: the current BSG situation recapitulates the ancient historic tension between polytheistic paganism and Hebrew monotheism. The question naturally arises: what’s missing from this picture? Or, rather, what’s waiting to step onto the scene?
Enter “the final five”: a mysterious minority faction within the monotheistic cylon camp. And how do we learn about four-out-of-five of their identities? Through their simultaneous recitation of Dylan’s “All Along the Watchtower,” a song that recapitulates the crucifixion as a sort of ambiguous existential farce, in which a “joker” Christ suggests to his thief companion that “there must be some kind of way out of here” as “two riders” of apocalypse approach in the “cold distance.”
Quite interestingly, once they find themselves standing together in the rectangular room, the 4/5 are instantly converted to the belief that they are cylons. The first four Disciples of Christ also decide instantaneously to drop what they’re doing and follow him. It is my thesis, then, that the 4/5 will turn out to be disciples of the final cylon model, who will be the incarnating son (or perhaps daughter) of the cylon God. Thus, the “two riders” are the cylon and the human species, heading towards an apocalyptic showdown at Earth; the “cold distance” is that of space; and the “way out of here” is a new path, a new beginning, a redemptive transcendence of the cycle of violence. But this will be a radical interpretation of the incarnation, in which the child in a sense defies and transforms the nature of the father (echoes here of William and Lee Adama) by creating a universal faith in which cylons and “humans” can recognize their common artificiality, their common “inhumanity.” So the messiah (whoever it turns out to be) is a “joker” of sorts, who reveals that the joke is on us.