Back in 2015, I wrote a bit about Cryptic Alliances as states in Gamma World.
I had some more thoughts about that.
States Aren't Cryptic
This is certainly true, on at least one level - states aren't secret. They can certainly be hard to understand or mysterious to outsiders, which makes even more sense.
One issue with defining the CA as secret societies is some just don't make any sense as secret societies. While you might get secret members in areas they don't control, secret Red Death members, secret Healers, and secret Bonapartists just seem odd.
I figure the Knights of Genetic Purity fly their racist flag like Ed Norton in American History X. They don't seem like they'd be shy about it (or see a profit in being shy about it).
At the same time, secret members make sense. Those out in the uncontrolled hinterlands, those in mixed societies too powerful to control for the CA (because of power, distance, proximity to another CA, or some combination of the above), those on special missions - those members should be secret. Secret signs and whatnot make sense. Give the secret sign, know the other person is familiar with your CA and knows the rituals.
Some Alliances Don't Make Sense as Secret
Broadly speaking, some alliances do make sense as secretive groups that wander the world. Others, though, don't. The Red Death, for example, or Ranks of the Fit don't make too much sense as secret. They make sense as small wandering groups up to large nomadic tribes or armies, but secret? It just seems to lump the ones that do make sense as secret groups with ones that don't.
Overall I like the idea of some groups controlling large areas and acting like states. I think it fits Gamma World well. It fits Jim Ward's original conception (even if he waited until The Dragon and not the rulebook to get that out there.) And I think it makes those cryptic alliances seem more threatening. A local spy for a large, violent, and nearby belief state is a bigger threat than a spy for a spread-out society. And even if a large secret conspiracy is undermining some neutral town or state, what happens when they take over? They remain secret? There isn't much reason why, anymore.
Take advantage of the weirdness that are these groups and make them both overt large threats and individuals who may be tied to those states or something else entirely. I think that's a very effective and interesting way to set up a campaign.