Cargo run and custom rosters are the main appeals of the game for me (without a bigger pvp scene). I really wish I could combine the two by having an option to make a (smaller) custom roster to use in cargo run.

Gotcha. Good point.
We ARE working on a new single-player mode right now, for release in our next update. It’s a much expanded version of cargo run, with you flying aorund the Reaches and having adventures.
We’ll see what we can do here to let you customize.