Cohesion is only intended as a mechanic to discourage "snaking", I think, since piracy doesn't do that any more. If you started adding other unrelated mechanics into the mix it'd probably lose its original purpose, and necessitate adding another small mechanic to accomplish that goal again anyway. Besides, I don't think it's a good idea to add penalties for having lots of factions. It already naturally makes it harder to please all of them, and weighing the demands of political groups is one of the more interesting parts of the game, so encouraging players through penalties to minimize how many there are and how much they interact with them would be a shame.
Cohesion does seem to be a strange mechanic though, it seemingly exists solely to counter one particular strategy, and if you don't stretch your empire in long chains all over the place it'll probably never have any effect on your game at all.