I still think it's been made that way, and is not modified. If an existing box had the extra height added, it's a bit of a coincidence that the extension is nailed together in the same manner as the lower part. Different colour timbers can be the result of using second hand materials, or having just aged differently. Old planks or floorboards can be different colours on opposite faces depending on exposure to light and useage.
Does the inside of the box have any signs (screw holes, glue marks, etc) of having ever had partitions, support blocks, turnscrews, or retaining straps?
Does the outside have any signs of how the lid was secured closed other than the current fittings?