The difference is in whether he cares about how you answer. The difference between informing and editorializing. Although, as you’ve said, after enough "Are you sure you’re sure?"s it certainly begins to collectively amount to editorializing even if each question in isolation is neutral.
And of course there’s always the question of whether his words matched his own intent. In addition to all the points you and others have made about whether or not you correctly understood his words.
See also this current thread for similar ruminations about understanding intent in conversations: