yes

Well, obviously with the empire intact and no real sequel contend (i would have uninstalled the mod otherwise) there can only be one "endgame" crisis and thats the Vong. Thou if one knows how SW turned out etc. one can counter them, althou the limit on Super Stardestroyers is sadly LOW (not like the empire had more than 10 executors at its height in total, with other dreadnoughts etc.)

Oh and one more thing : why is it only the empire gets to use her? Lyusankya was obviously captured, among other ships, so i would make them available for the rebels too, althou hidden behind either an ascention perk OR some other stuff that needs to happen (event wise, as was in the Star Trek new Horizons mod. You could get her via event lategame etc. or build more on the institutions , so the rebels can POTENTIALY capture imperial assets (or from others).