The docking ship is what you use when boarding derelicts, because the mother-ship is either too large or too risky to dock itself. This ship contains the drones you use to explore the derelict, and whatever you've collected during the mission goes back with it.
The docking ship is always referred to as 'R1' and is effectively a safe point, because, for example, slime cannot infest it, and this room is never susceptible to random radiation leaks.
It is possible to relocate the docking ship to any of the other explored airlocks if the need to do so presents itself.
While the docking ship can still relocate docking points with a hostile infestation in it, it cannot leave the derelict if so.