Official comment
Map Pilot keeps track of the last location it was in contact with the aircraft so in the case of an app crash you can RTH and relaunch it and it will go back to the last place it recorded the aircraft being.
We will be adding the ability to define a waypoint at which to restart in an upcoming version.
In the case of Battery Limited flight, it is possible to throw a warning that the aircraft will be executing an RTH soon but there is no way to cancel it. Once the battery tells the aircraft it needs to head home it is going no matter what.
In the case of time limited flight, we could potentially extend it but that seems a bit at odds with setting a time and then overriding it. It is kind of like setting your alarm clock for 5 AM and then hitting snooze until 7 or something.
There is a waypoint at the beginning and end of every mission we create. What is the purpose of what you are trying to do here? In the next version of Map Pilot we will be automatically bisecting all flight legs over 2 km to allow for longer flights and keep you from getting stuck when the aircraft heads home for a battery change when you are way out.