It's feels silly to have such non-consequential items in those chests. Items that are readily available everywhere in Eorzea. By getting rid of the fluff items, like clear prisms and potions, and replacing them with a minimal amount of tomestones (like 5 or 10) or gear would make the dungeons that much more rewarding to run. It would also have the additional effect of keeping inventory space that much clearer.

Summary: make 4-person dungeon chests ONLY contain either a small amount of tomestones or equipment.