One issue is which NPCs would be available lore-wise for a given dungeon. Just to throw out an example, Bardam's Mettle. While they could easily have Hien or Gosetsu fill the tank role, and Lyse as DPS, you have no healers available. Y'shtola is back in Eorzea and the twins are busy with the Doman Resistance. (I mean, we're also ignoring that Bardam's Mettle is supposed to be done alone by Xaela tradition, but the game quietly ignores that anyway.)