Two things
1) Fort Joy is relatively recent.
and
2) Not only did they not create the torture dungeon themselves (they are working out of the old fortress), BUT that isn't anything special.
1) But that's the thing: apparently, it isn't. In the seeker camp by the vines to the bell is the lizard Bahara who says that she "was like you once, a lost soul driven by instinct from the bowels of Fort Joy." and that she has been at the Sanctuary of Amadia for "several years".
I could ignore the debris in the prison and maybe even some of the makeshift nature of the Magister's non-living-arrangements if Fort Joy was only very recently taken over and repurposed, but I can't ignore that if another part of the game says it's been several years.
Anyway, it's still a problem if Fort Joy has been open for only one week. Guards would still need places to eat and sleep. I realize that game worlds are an abstraction and they can't show every house in the village needed to house the 50-100 NPC's who roam the streets, but it's hard to ignore the facts that the prisoners have tents and bedrolls, and a kitchen and storeroom, and the guards do not, despite the fact that the prisoners are supposed to be the poorly treated ones.
2) I'm not talking about the rest of the island and Braccus's old ruins. I'm talking about "The Flenser's Playground", which is in Fort Joy's basement without even a locked door in front of it. You can't credibly tell me that has nothing to do with the Magisters.
