The Ballad Index notes are misleading, probably because they have relied too much on secondary sources. They seem to imply that Stevenson got the verse he quoted from Charles Kingsley's book, the full title of which is At Last: a Christmas in the West Indies. He didn't: all he got was the phrase 'The Dead Man's Chest'; the name of an island. Writing of the Virgin Islands, Kingsley said:

'Unfortunately, English buccaneers have since then given to most of them less poetic names. The Dutchman's Cap, Broken Jerusalem, The Dead Man's Chest, Rum Island, and so forth, mark a time and a race more prosaic, but still more terrible, though not one whit more wicked and brutal, than the Spanish Conquistadores, whose descendants, in the seventeenth century, they smote hip and thigh with great destruction.'

(Chapter 1: several facsimile editions can be seen at the Internet Archive: texts.)

What Stevenson meant by 'a dead man's chest' I don't know, but the line would make best sense if, like Kingsley, he was talking about an island.