Perhaps Tommy could not let the truth stand in the way of a good story.
There was a lot of trade between Newfoundland and Nova Scotia with the West Indies and fish was often exchanged for rum. Today most Newfies just smuggle rum in from St. Pierre , an island belonging to France a few miles of the Newfoundland coast.
In any case the song is fiction but probably influenced from some true events. The salvage methods described by Stan are a more recent technology than the old schooners that would run to the West Indies.
The names Mary, Ellen, and Carter are all common here in Nova Scotia.