Even though TESO isn't exactly lore-friendly, I doubt they'd imply any mortal could be more powerful than the tribunal, especially during this time period. It is much more likely that the dunmer will be represented im the ebonheart pact by a hortator or something similar. ALMSIVI will make an appearance, obviously, but they wont directly intervene in the war effort unless morrowind itself is somehow in danger. They are RELIGIOUS leaders after all, and dunmer have always had their own political leaders as well.
While we're on the subject of morrowind, was it even called morrowind in the second era? I thought it was called Resdayn. Off topic I know but that thought just came to me.