You're collecting the wrong chests. The Quest is poorly worded, and doesn't really explain what these "faction" chests really are. . But the gold region chests and the chests that drop from public events or world bosses won't cut it. The chests you want are blackish-green with green backlighting. Most of them are on top of the various hills and elevated structures in the Miasma. Put a chest finder with the widest radius possible on your ghost, and it will show you where they are when you get close.