As much as >>96838920 point about FTL is valid within the same setting (best FTL win) it's just meaningless to compare distinct setting.
All those "who would win" thread, only have one interesting outcome: finding the right set of circumstance or enemies to have an interesting match to talk about. Having a victor isn't even relevant.
Me, I say the Lunar War setting beat Starwars and W40K. As they appear somewhere the laws of physics collapse for them and they all die.