In the first season, it was also established that the Machine refers the "relevant" cases to the appropriate authorities by subtly rewriting intelligence reports to lace them with information highlighting the Person of Interest. This was done so that even the people acting on the Machine's intelligence would never entertain the thought that there was a Machine. Obviously, the Program that Shaw worked for has been cutting out that elaborate middle man and grabbing information directly from the source. We know that Root's boss at the Office for Special Counsel is one of the few people alive aware of the Machine's existence, and we know that he oversaw the Program as well. It's possible that whatever direct access he has is as limited as Finch's own access. One gets the impression that the Program isn't exactly on the books. On the other hand, it's possible that the Program gets a great deal more information than that, and only chooses to give its operatives a SSN. It also raises the plot question: how does the machine handle foreign nationals that aren't American citizens and thus don't possess a social security number?