I tried to complete this quest but found that I need high Metaphysics score to reach the best outcome. So I stopped in the middle of the quest: after I talked to Guildmaster Mairu, but before killing Nagas with her rod (because after the rod is in my pocket the quest can't be interrupted). But now, when I gained levels and improved metaphysics, I returned to this quest, but even though I have the rod in my inventory, the door can't be opened - there is no option to rotate a code dial.
Saved game: https://drive.google.com/open?id=1InjKAPSKZwnqCfT-uidoPXKUJQlb8tBS