Again, I'm just going to put it down to gameplay and story segregation - narrative wise you only ever travel into a dungeon or raid or duty once. Concepts like Duty Roulette are ignored by the storyline.
The only times you travel back into a dungeon a second time are for the hard mode version (the hard mode storylines are usually attempts are made to clean out or restore the dungeon after the player went into it, only for the authorities to discover we didn't really do a very good job and that there is still something evil in there, and we're roped into dealing with it). So narrative wise, repeating a dungeon is ignored by the game's storyline, you only ever fought through it once.
"BUUUUT ENKI!!!" I hear you say. "What about things like atma books directing you to do a certain dungeon? Or the anima weapon quests doing the same?" Well, again narrative wise that is not actually part of the story despite appearances. You're being told to enter it by a game menu, not part of the storyline. There are situations where sidequests involve a certain dungeon (specifically, some of the Grand Company quests coincide with a separate sidequest to unlock the Aurum Vale and Dzmael Darkhold), but those seem to be exceptions, and even they can be handwaved away that despite being separate stories, actually are concurrent in the narrative (in other words, despite accessing those quests separately, story wise you did them both at the same time).
This was confirmed back during one of the Fanfests when Ferne explained that the game's narrative does not flow according to how the player might play through content - it instead has it's own set narrative flow that ignores gameplay (this was specifically used to explain why a player could do the level 50 CUL quest featuring making a meal for a certain Sultana of Ul'dah, even after having done the 2.55 story where... you know.. she was kind of put on a bus for an extended period and considered for all intents and purposes, deader than dead (of course that particular bus came back, but we didn't know it at the time.).
So basically, regardless of how you undertake content in the game, the game's storyline has a specific, structured chronology that ignores in what order players may actually undertake it, so a little suspension of disbelief is required here to make it all work.![]()