The issue is not related to the main story progression, which is the only thing that is affected by the progression settings. We still have to turn in side quests separately, even if our friend turns in the reward after we both complete the quest. That in itself is fine, but the display of the next side quests steps is what is missing from the map on a number of quests for us. We don't see quests we should be seeing, as confirmed by our friends who did get the quests. We feel this is related to how multiplayer is handling when story quests are completed (which is what will unlock the next side quests if you are caught up on them). Most of us most likely progressed like: Do story in multiplayer > Completed Story Step > Friend Identified Side Quests are available > We ended session to pick up all side quests > Rejoined session to complete them > Moved to next story step. This pattern worked fine for the early quests, but the reported missing quests seemed to have gotten lost amongst this.