That's part of the reason why I've always found the idea of factions possessing any real kind of power amusing. It's all an illusion. As for the second example, incompetence is generally speaking 99% more common than malice. Think it over.
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So no power ehh?
So Admiral Hale is in NY, he tells all the indie BSs around Manhattin that Navy ship lets call him BOB is a traitor. Kill him now. What do you think all the idies are going to do?
Now an indie "Admiral" tells all navy ships same thing, and what you think happens?
So they do have power, as most indies in this game seem to think the "Official" factions are gods to be followed at all times.