Sure, but if for some reason you have to forfeit the game, your sister-faction doesn't get to automatically absorb your systems.
Say we have two IR factions -- player A controls 3 systems, and player B controls 3 systems.
If player B drops out, player A doesn't get to take player B's systems by fiat.
If player B wants to then join player A (perhaps acting as an extra helping hand by commanding a ship or two), then that's cool, especially if Player B still wants to be "in the game" as it were.