The act of covering food is actually a survival instinct left over from the wild. When a cat finishes with his prey, he may attempt to cover the remains so that other predators aren't drawn to the area and more potential prey aren't alerted. It's the same instinct that cats have about covering their waste. It all comes down to survival.
The act of dropping toys in the food or water bowl is due to the cat considering that area as his safe eating-place. After he has "killed" his "prey," he deposits it where he's used to eating.
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