A faction on every Freeport, and a Freeport for every faction.
And each of these groups mind their own business, their own economics, and maintain a set of allegiances and diplomacy that fit their location.
In other words, Freeport 9 would favor the Corsairs.
Freeport 10 would favor the Outcasts/IMG
Freeport 2 would deal between Rhienland and Liberty
Freeport...you get the idea.
Things cant exactly follow the utmost of logic all the time, you know. If we go by that line of thought, over the centuries the population of each Freeport would have been absorbed into the groups that they support. Small, fractured factions rarely survive for a reason.