Bullshit! The alternative is mentioned in the article, trust the official documents presented by the 'suspect', as that's the purpose of the documents. As in OP's quote:

“ICE officials have told us that an apparent biometric match by Mobile Fortify is a ‘definitive’ determination of a person’s status and that an ICE officer may ignore evidence of American citizenship—including a birth certificate—if the app says the person is an alien,”

"Trust the word of the black box" is pure technocratic dystopian nonsense.