The rules of US elections are fairly well spelled-out, so low turn-out results are not contested. In this case, Congress would need to make the decision that i

The rules of US elections are fairly well spelled-out, so low turn-out results are not contested. In this case, Congress would need to make the decision that is in keeping with the "people of Puerto Rico". If you read further in the referendum link you posted, there are a number of reasons why the referendum was boycotted. I doubt that Congress would want to jump into the middle of such an ambiguous situation and declare Puerto Rico a state by fiat.