In GC2 we had a very good idea of what went into the score, right down to the exploit of building a huge array of military starbases.
In GC3 as far as I can tell the developers have given us no clues whatsoever. Is it linked to faction power? Probably. Is the score higher if your faction power is 20x the 2nd place faction rather than 10x? Maybe, I haven't been able to tell. Do different victory conditions have an effect? Who knows? At this point I just ignore the score, and the metaverse.