At any point the pilot should be ready to take over if there are flight errors. Map Pilot programs the aircraft with a set of waypoints it will fly, it doesn't fly the aircraft. You could try using the Stop button but that might not work on the take off leg of the flight.
All flights in a mission start from the home point on the ground. From there you can choose where to pick back up if you don't want to restart at the designated abandonment point (blue dot) using the Manual Restart Point feature.