Andarian, something I was wondering: what exactly did the difficulty settings in Sanctum do? They set a localint to indicate the difficulty which presumably other scripts drew from...was it simply finding better items on easier difficulties, was it less monsters, was it easier monsters, etc?
Most areas that contain difficult combat (especially in the ruins) specify an onEnter script named "sa_adjust_combat." The first time the PC enters, it iterates through all objects in the area (especially creatures and encounters), checking for certain variables that have been set on them. Depending on the variables found, it will do things like delete the creature/encounter, "weaken" it with permanent stat lowerings and/or HP damage, or scale the encounter difficulty. If you look over sa_adjust_combat and the scripts it calls you should get the idea.
The approach does allow the player some flexibility in adjusting the combat difficulty during the game (using the Adventurer's Guide), but it's not perfect. It works for areas the PC hasn't entered yet, but those settings become permanent once the player does enter them for the first time.