The place to get the best gear is Umbra exchange. The best ways to get enchanted items is rescuing captives and asking for material reward, or opening treasure chests or hidden sections.
The Cultists' Hideout and Marsh are probably the best places for farming gear, but are each are quite difficult. Though if you are after some specific types of gear(especially for mid-range gear), there can be some better locations.
The dragon and cult leader can only be defeated once. The entity can be defeated an infinite amount of times. I just exit and go back in immediately when farming the area.
