Actually Samura is the main power of the Kusari government, not the KNF, the KNF is just Samura's thugs pretending to be legit.
The issue isn't that the AFA and the KNF are both run by Samura, that's not really how it is.
The FA isn't controlled by Samura like the emperor and KNF, the FA are farmers with their own agenda, being manipulated by samura against synth foods. If synth food ever is driven out of Kusari, Samura will crush the FA to continue their monopolization of the food supply with their own genetically modified rice.
So there is a whole dynamic there that isn't being played. You call it a shadow deal, but unlike the real shadow deals you mention the AFA act like they belong to the KNF openly. That openness means the FA is no longer valuable to Samura, because the cover is blown and everyone knows the AFA is simply another word for KNF now.
That's why you should work seperately from the KNF (In agreement with the rules of your ID as well)
That's a dramatically different situation from the CG and BD who are both pirates working against the illegitimate, samura run government of Kusari.