In regards to a 1000+ clan, honestly that won't even put a dent in anything except perhaps a duchy. We're talking easily over 10000+ players per kingdom here.
Huge empires are a pain in the ass to manage and when a thousand counts, former dukes and former kings are lighting the torches and gathering pitchforks, legitimized by CBs then you've got a problem.
Now will some groups dominate a location, a town, a county or perhaps even a duchy? Yes, most certainly. That's a good thing. It adds conflict, color and story. Will one group manage to control a server? Sure, it's possible, but you try herding over 10,000 players into one cohesive unit. It's worse than herding cats :D
What SBS has stated in interviews is that they will keep an eye on things, but essentially the Soulbound Engine is the GM, which means that it should address major imbalances through story events.
Now if things get totally out of whack, they said they'd step in, but otherwise we should manage things.
Equally they said some things in the game might change due to our actions, quests, mechanics, cults etc... However it is supposed to be our world as well, the world we make of it, we create and form, and since many members of the team do plan on playing the game, I imagine they'd rather experience the game as a game, rather than as a GM.
After all if the Soulbound Engine is good enough, it'd throw even them for a loop.
So I wouldn't worry too much on feeling the grasping hand of a GM and focus more on planning and eventually playing :D