It far surpasses that. He wasn't flying that S-3 Viking, he was just along for the ride on Navy One. No different really than riding on Air Force or Marine One.
This was spur of the moment, think quick time, while the carrier landing was pre-planned. This tells a lot more about The Man.
Actually he did fly the plane about 1/2 way to the aircraft carrier. There's a really amusing anecdote about it in one of the books about him--can't rem. which one but someone will know.
The SS agent asked the navy pilot as they got on, "You're not going to let the Pres. fly, are you?" The pilot assured him "no" but as they got to cruising altitude, the pilot let the Pres. take over. The Pres. then proceded to mess around a little, losing altitude, to further make the SS guy nervous. (this might not be exactly right, but when I read it I LOL'd because I can just see the Pres. enjoying making the SS guy a little nervous.
As you say, tho, this happened in seconds while the aircraft carrier landing was totally planned.