I understand what you two are saying but you are missing the point.
For starters, I don't agree with GM's having more power than an FM (Given that FM's are in-charge of running an ENTIRE faction, while GM's ONLY have to worry about their plot). By this, I mean that they shouldn't be allowed to do whatever they want with another faction, this is espically true when a GM decides to misprotray the other faction.
All we FM's ask, is that you take the time to communicate and talk to use FM's before you use the assets that we've created for our faction - but also - so that we can help you understand how those assets would function.
Taking the military ship of one faction, and using that ship to attack your plot-ship, without even bothering to talk to that faction's manager. Or taking a group of soldiers, and doing the same thing, will lead to drama and problems.
I remain of the mindset that GMs are the principal entertainers of players on this site, and therefore should have the most power. Fred's "factions as PCs is wrong" theory also holds true here, and these "rules" reinforce that.
Not true Doshii, and it really does sadden me that you think this way.
You're right, faction's are not PC's... however, that doesn't mean that a GM should have a right to do whatever he wants with the faction, possibly even going as far as going against how that faction operates culturally.
And the rules do not reinforce it, all these rules do is help ensure that FM's for factions are talked with so that they can discuss how certain assets can be used. In a way, this also helps ensure that no one can take military assets from one faction (Say, a Nep taking Yam military assets) and using those Yam military assets to attack the Gartagans in an effort to try and create a war.