Hello, I've never heard "had been born" before as well,but according to your setence,I think because it talks about actions in the past,there was maybe a necessity to use what had happened before that time.. He had been born in that city;he hadn't returned there for twenty years,then there came a time when Fausto Ruiz got off the boat at the port of that city. I guess it's because of narration,the past perfect is used with "born".
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Exactly what i am searching but still i don't know why they use had been.