Ruined City of Arah (Story) and Reward
The champ boxes only have rare chances to drop things higher than masterwork quality, and MF doesn’t affect the contents of containers (such as champ boxes).
As for the rest of the reward, the reward for Arah Story is exp, karma, the class-related level 80 rare helm, and 50s. You should get the 50s reward, exp, and karma every time you run it for the first time in a day. The helm is a one-time only thing, and the shards (3 of them) I think only drop from a random boss in the dungeon. And that big chest on the deck is the same one from the objective you did before killing Zhaitan; so it won’t have anything in it at the end, unless you just didn’t get your loot from before.
You don’t get your main reward (the pact token, guild influence letter, siege blueprints, etc.) until you do the follow up story at Fort Trinity.