I think in this case, Sample 1 works best. The clouds obviously repeat themselves but I like the way that it gives the impression of there being several cloud layers. Sample 2 just plain looks wrong and Sample 3 is too empty to me.
For the final background, if it's possible to do so, you might try and actually use a transparency layer for the clouds, which would look just like in the game, especially in the area of the moon. It's just a suggestion though, so don't waste too much time on it.
As for Revned's custom work in one of my room, it annoyed me only because I knew it was a 'hack' and nowhere near a true repetition but I've accepted that such a repetition is impossible to achieve without cheating.
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"With the first link, the chain is forged. The first speech censored, the first thought forbidden, the first freedom denied, chains us all irrevocably." [...] The first time any man's freedom is trodden on, we're all damaged. - Captain Jean-Luc Picard
B*tch, meet reality. Reality, meet b*tch. - Me