The orange survey area polygon is the area for which imagery is collected. The way Map Pilot does it is optimized for Maps Made Easy use. If you feel like that is cutting out important imagery you can use Connectionless mode in your mapping which will collect the imagery at the turnarounds.
You should cover the area you want a map for with the orange polygon.
The auto trimming just takes off the jagged edges that end up being areas of low overlap. If you want to leave them you can trim them for the web maps after the fact: