There's a difference between change and complete change in direction, power, and goals. The Zoners exploded in power in the past two decades because Igiss thought they were actually several centuries older and several order of magnitude more populous than they were in vanilla. Every other reason is just a justification found to rationalize this.
If we did things again, I would not support many of the changes that were made in previous years under that assumption- notably, the inclusion of Zoner warships. However, what's done is done- the Zoners have warships, though they are so spread out that they are still should need to balance on knives to avoid the wrath of anyone in particular. Like the GRN, who don't have the ethical bindings of the other houses and see no reason not to flatten you... you shelter and supply criminals, after all. (Remember, in vanilla, Liberty was on the verge of annexing a nearby Zoner base unless the Zoners closed docking rights to criminals.)
The main issue the Zoners face that can actually be addressed is the perception that they are a unified force to be reckoned with. Declaring war on the Zoners is not something most people can do casually, but that's not because the Zoners could actually overpower them- for one, the concept of a Zoner offensive is insane (though banding together for defense is quite reasonable), but also because just about everyone- Zoners included- is taxed to the brim as it is. No one save the Houses can casually declare war on anyone (and they can't casually start wars with each other); it takes some serious grievances to justify such a risk given the precarious state of Sirius. (Active alliance with one's enemies might be considered a serious grievance.)
In truth, the Zoners are more of a confederacy than anything else- if a member of the Zoner Alliance decided they didn't want to take part anymore, no one would use force or economics to try and stop them. This is not to say that they could act with hostility toward the Zoner Alliance without arising their ire- the ZA would best treat them exactly like they would treat an outsider.
There are a few other huge points that go along with this, of course. For example, I really don't see why the various Zoner groups would send military aid to each other for anything that doesn't threaten all Zoners (remember, just because the Zoners are not internally organized as a unit, doesn't mean that outsiders won't decide that getting rid of one group of Zoners is any different from exterminating them all). Remember, confederacy.