Don't work too hard at this.
The simple answer is that the writers don't know enough about science and astronomy to make up realistic concepts.
"This isn't God, it's just a super advanced being who can create matter and life and perform miracles." Sorry, that's a cop-out. Calling God an alien without changing any of his other properties really doesn't change the concept.
Roddenberry used the same dodge. Anybody ever wonder what happened to the seemingly endless number of near-omnipotent beings that the Star Trek original series seemed to run across? "Q" was the only remnant of this kind of idea that drifted into "The Next Generation," and that's probably because Roddenberry was still calling the shots. Heck, what happened to the Organian Treaty?