There is an overall policy that the Enchanters set for the Circle.
They do meet from time to time in Cumberland to discuss Circle policy. It is at one of these meetings that Fiona voiced her belief that the Circle should split from the Chantry.
She has also been to other Circles, not just her own.
So, she has met other FE's many times, at least through those meetings in Cumberland, she has visited multiple Circles, and she is all about politics and the Game, so I'd assume she knows more than she lets on.
Does she know everything about all the Circles? Doubtful.
Does her opinion and beliefs affect how she views the Circle, its policies, and such? Of course, just like how some people focus on the bad things about the Circle because they believe it is bad and how I like to focus on the good things because I like the Circle system.
People on here have even defended the Qun at times because they focus on the good parts of it.
However, just because she has bias doesn't mean she is lying or mistaken, it is just another way mages can view the Circle.
Edit: I just want to mention again, that just because mages can get permission, it is unlikely a FE will give it, since people outside the Circles don't want a bunch of mages running around. Also, it is more secure to live in a Circle for most people who do not have ties to nobility. Some have no connections outside the Circle, so having them just be vagabonds would be silly and irresponsible.
Templars were encroaching on the roles of the Enchanters and the daily operations of different Circles, so this did cause issues in some Circles. However, just because Templars were forcing themselves into running Circles doesn't mean that was official Circle policy.