Just make "objectives" list - defeat x amount numbers of certain enemies, get certain amount of tomes. And make the Boss battle as the bonus round where it gives additional more tomes that are must be completed to bump up the amount of rewards. This way players have to hunt down the enemies to complete the objectives or it will severely undercut the rewards potential. Also for each objectives completed you get 300 gils, so you end up with 3000 gils per dungeon if you complete all objectives and boss battle. If we have to do the dungeon for twice as long then the reward should be doubled. Also make those mobs drop random end game crafting items for better weapons and random materias tier 3 + 4.
Basically make each end game dungeon runs as "multiple levee runs" with gil rewards, item rewards, and additional tomes. You already have the mechanic of these "killed x amount number of enemies" in the game, why not use it.