Wow, managed to fuck that up even though I'm sure it looked alright in the preview.
It should read:
"Any sufficiently advanced technology is indistinguishable from magic". However you can differentiate based on the assumptions each argument makes.
The difference I can see in the two is one assumes that a race after a large period of time developed technology that we see as impossible. A fair assumption, as we can see this in our own recorded chronology.
The Supreme being makes a much larger assumption, the supreme being must somehow exist outside of the rules that all the other characters live by, and be able to affect those who are constrained by those rules. We cannot see this from our own chronology, or anywhere that has not later been re-explained, and re-attributed to something living within the rules of the system, through investigation using the scientific method.
This is what I see as the difference between the two, and why for me, any explanation that amounts to "God did it", or "It was all a virtual reality" will be a cop-out (both situations where something exists outside the set rules of that reality). Especially in fiction, when you can make up any plethora of more exciting endings, which fit.
However, you could argue that this ending does fit the series, as it is constantly mirroring western theology, and implying someone knows what's going on.