Best example would be the Aeternus Continuum. They are a “society within a society” for both ISA and Marchers.
But right now, the ISA and MW are your two main political entities. And, as you mentioned, the Khazaraki Host is out there somewhere.
Through history there were various factions, but these rose and fell, resulting in the alliances we see today:
1st 1k years or so, its just humanity trying to survive and figure out gates between worlds, period.
Then during the Sorrows you get the Morrowan League, which pulled together disparate colony worlds separated in the cataclysm. Alongside the Morrowan League are alot of “city-state” worlds and coalitions, many of which culminated in the Orellian Republic, which opposed the Morrowan League’s ISA style “join-or-else” approach. The Morrowan League ended up crushing the Republic, but fell during the “Whispering Death” plague (AC founded around this time).
Most “wraith fleets” also seem to date back to this time or earlier.
Following the collapse of the Morrowan League, society collapses back to city-state worlds and small wars between them - almost another 500 years, until the rise of the Caspian Federation, the Rachlavsky-Laris Combine, the Mechanist Assembly, and the Khazaraki Host. During this time you get the Khazaraki exodus, fleeing whatever they found on the fringes of what would eventually be the Marches. The Caspians and RLC move in to those territories and establish outposts (you can probably see where that goes). You get a couple border wars (with the Marches officially established vetween those wars) the RLC collpases and devolves into the Free Workers Union, and the Mechanists are defeated and discovered to be baddie war criminals.
The Free Workers Union ultimately collpases, and the Caspian Federation is the sole major power. It ends up being too unweildy and collapses under its own weight, helped along by a Khazaraki invasion - the Malgur Host. The Malgur destroy the Caspian homeworld, but at great cost, and both are done.
The ISA pulls together in core Caspuan space. The Marches have been independent for some time here, too. Naturally, the ISA want to try and retake all the old Caspian planets. The MW form a coalition, and thats basically us.
But I think over all that history, its clear there have always been independent planets or small coalitions, connected via gate travel, and even within the ISA there are faction. Certainly, the Marchers are not a big happy family, they are loosely allied worlds with a common enemy (or three) but lots of different cultures.
I think thats on purpose to allow is room to tell stories, and allow for narrative expansion. But with so many different worlds, youre bound to have disparate cultures and alliances, even within the “great power” factions we have. And with how worlds are connected by gates, and not real space, those can be all over the galaxy. It depends on what gates connect which worlds, and how reliable they are to travel through.