If you're looking for precision, in flight waypoints gets the job done quicker.
In Flight waypoints will allow for more precise, lower, closer shots.
To get a similar shot with Flight Plan you'd still have to use up a battery and more.
Flight Plan has it's advantages as well as in flight waypoints.
All depends on the shot you're looking for.
Try a similar shot, 2:46 to 3:00 min of this clip in one go using Flight Plan.