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You're in a Jailkeeper's ship so... could it be the panels are displaying the prisoners and their status? Maybe a green light means the prisoner is still safely in custody, but a red one indicates they escaped? :o

I'm goofing around, but don't worry: you've already defeated the boss with the green light. (It was the big eye thingy! That panel is a bit of foreshadowing for the final boss, and one of the many hints for the shocking reveal!)

I'm guessing the item you're missing is a Trophy, either for a secret boss or the reward for collecting all the Strange Eggs. If it's one of the bosses, one of them is behind a closed door in the temple, and the other is buried under a tombstone. Hope this helps!