How is score calculated?
Solution 1:
According to the in-game tips,
Your score is based on how many ships you defeat, the number of beacons explored, and your total scrap collection.
The actual equation is 20 × Ships Defeated + 10 × Beacons Explored + Scrap Collected.
Solution 2:
Difficulty is a flat bonus, I believe 25%, to offset the equivalent scrap bonus for easy. The precise value IS listed somewhere on the official site if someone wishes to go digging.