All of the Beyonder's origins are true
Ok, we can assume that the first origin story is true, and the Beyonder was truly the most powerful being to exist in the Marvel Universe—the sum total of a universe. This being desires to understand desire. A being on the Beyonder's level of power would be easily capable of time travel, reincarnation, and splintering of his life-essence into several beings.
In trying to understand mortals, he could easily have traveled back in time and become an Inhuman for example, or allowed himself to be "convinced" that he was a Cosmic Cube and become a part of Kosmos. All part of understanding what it was to be mortal and to desire. I'm not saying that he was faking his apparent lack of power, but everytime we see him as weaker is after his apparent death and resurrection. Most of his former power could have been expended in that act.