NA (code 3) is for purchase loans and when the applicant is a non-natural person (an entity).
There's much debate about this, but knowing what I just stated above (from the FIG), you have to code everything else as a 1 or 2 (that's the camp I'm in). Face to face applications could be a 1 or 2, depending on if the applicant completed the info or the loan officer did. Non-face to face applications would always be code 2 (No - the LO didn't complete the info based on visual observation).
Some say their software automatically puts code 3 for all non-face to face apps.