Ahhhh, tropes. I can do tropes. I know Trope Fu.
As to it being magic, perhaps you're right on this count, but regardless of what the explanation is, we still ought to choose one. Not doing so is just bad writing, and akin to a version of Powers As The Plot Demands It, except applied to an entire species. Having the entire rest of the game be entirely realistic and leaving one element of the story unexplained is a Plot Hole, which is a sure sign of a writing problem. That's precisely what we're trying to avoid in this thread.
Yeah, I don't think travelling faster than the speed of light is at all possible, nor do I think gravity manipulation will ever be possible, and especially not matter replicators or "beaming" as a form of transportation, to list a few other things. It's considered an Acceptable Break From Reality. Even so, I, and most people, like there to be an explanation behind the technology in a particular story - and I doubt this could be considered Fridge Logic - people are going to come up with these questions while they're still playing the game. Asking, "How does Captain X manage to fly his ship around the galaxy so fast?" and being met with, "He just does" doesn't exactly help with the Willing Suspension Of Disbelief. The Rule Of Cool can help here somewhat, invoking the MST3K Mantra, but that mantra doesn't apply at all when you're trying to make the rest of the universe as realistic as possible. A work that strives to be serious in all areas can't leave one area unexplained without raising questions.
And no... your One Big Lie didn't really make much sense from a physics perspective. =P However, One Big Lie is supposed to do that, from what I remember... but you're also supposed to follow up whatever laws of physics you invent to logically work out the effect it has on the rest of the universe, and not just leave it as "this is how it works, now let's move on."