Title.
I'm 2nd on Score (testing custom faction to see how well it plays), but not on any of the Faction ladders because I'm using a modded (.xml) faction rather than a custom one. I haven't tried it, but I imagine if I copied the faction in-game and played with that (ie, a .faction faction) it would register as custom. I'd also guess that if I had modified an existing faction, it would also register correctly.