That still does not account for the fact that Miami is 7th in blocking punts and that Tannehill was getting beat up by our defense. At that point in the game, they have no reason to believe that Tannehill would be able to score twice with 1min left. But they do have a reason to believe that Miami might block a punt.
I don't think this is what they would do versus Brady or even versus Eli or any other dangerous QB. They would punt in that situation. But against Miami, they probably gameplanned this situation, thinking that they would not allow Miami to beat them in special teams. For instance, that silly squib kick before the half to prevent a special teams return bit the Cowboys in the rear. But for the end of the game, it was the right call.