Why the aircraft will continue flying to first waypoint if the pauseMission method is called in waypointMission?

This is the design. The waypointMission will actually start when the aircraft arrives the first waypoint. The waypointMission will end when the aircraft arrives the last waypoint and executes all actions. So the flight route from the take-off point to the first waypoint is not included in the waypointMission, thus calling pauseMission will not take any effect. If you want the aircraft to hover in air when flying to the first waypoint, user can press the pause button on the remote controller. Also you can set the first waypoint right on top of the take-off point, then the aircraft will actually starts waypointMission after the take-off action.