i prefer the way they did toto rak, they could do something similar but instead of finishing the dungeon when killing one of the three bosses i prefer killing all 3 to get the 5th chest, might take longer to clear but at least will help getting different setups, they can even make bosses more difficult as you kill em, 1st normal, 2nd double difficulty, 3rd tripple difficulty, idk or add more skills to those or in a better case make different bosses not just in name, of course if you're doing all that the drop rate should/must be upgraded according with the number of boss killed.

The best way to do it is make 2 rooms for boss pop, and a third room that is unlocked after beating the 2 boss, give 2 chest one chest per room and 3 in the last room (those 3 will spawn if all the puzzles were solved if not just 1) that would be a good time sink