Boy, did I miss a lot whilst I slept (and also during the years I stopped reading comics).
So, if I did all my catch-up reading correctly: basically, the Marvel Minds of Creation did do some column-A and column-B picking (eg, chakras with Kabbalah??). This not only produced an in-house mystical system sorely lacking but also screwed up Marvel continuity (hence all the retconning); and all this because of one-upmanship within Marvel (though perhaps also with DC in mind), to make stories "bigger" but not necessarily "better."
I still say: Beware the Fallen One ("Rabbit," indeed...c'mon)
What/whoever started the 616 universe: did that Agent also start the Marvel multiverse? And since a) Marvel is aware of the DC universe (multiverse?), and b) DC has its own manner of Big Bang ignition; is there yet some unspoken conflict between the two means of universal/multiversal creation? Put another way: let's say Eternity began one multiverse, and DC's Whoever started that multiverse...any acknowledgment of who began the Omniverse? How would the Phoenix Force fit into this picture? Or am I jumping way ahead of the game plan, going where Marvel and DC angels fear to tread?
As a final thought: Marvel might've done better to forgo any mystical approach and go with quantum mechanics, especially quantum cosmology. This woulda had the advantage of coming from a scientific system to explain creation and parallel universes and whatnot, with less room for fudging. But then, maybe that's why they didn't.