Why couldn't they shoot it down before it flew over land but after if flew into airspace? What is the national security benefit of waiting for it to fly over the country first?

My guess is they hoped it would pass over mostly unnoticed but then they saw people picking up on it and decided they had to get in front of the news story so as to not look incompetent. Then once the news story picked up steam their hand was forced by the jingoistic media circus and domestic political reality to take action.