Why do Shaper transition area mobs still drop no loot when Jonathan says that would be a chore?

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This comes down to the core of ARPG itemization as well. One of the reasons why it's good is because the next rock you turn over could contain the Mirror drop.
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Let's just say that all the monsters in a map drop nothing, except the boss. Killing all those monsters would feel like a chore because there's no chance that would ever return anything for you.