Idea is that the main portion of the starfighter would have been built in space, and the cockpit capsules would later attach and detach to change pilots; tag-team approach to manage prolonged time in space. (... and yes, I did finally find a use for those collectable minifig stands ;) )
The only part that contains a pilot is the capsule. The "docking station" is the rest of the ship when combined. I figured you'd want a seperate pilot capule for evasion/re-entry. The rest of that stuff would be cumbersome, so it would be left docked at a space-station until reused. It has the missles, as well as the satellite dish for communication (or jamming enemy drone control signals), and the numbered tanks/engines on the side are also meant to detach as projectiles in desparation. Also thought the solar panels would help recharge it if it is left in space.