Why in the world would you ever consider leaving you freighter and/tech 2 hauler podless in space!
Maybe leaving it space is not for everyone, or anyone? But at least you can bring a nimble hauler with you, dock, whip it out, and then scoop up any items in stations in the system, then attach the two again and move on to the next system, until the freighter is completely full. It will be up to the player to determine when its worth whipping out the nimble hauler or not. In some circumstances it will be beneficial in others probably not. But it would be cool if it was possible.
RE: the NPC hauler thing. Part of the UI could mimic industry UI, since it will take 1 minute per jump. So 20 jumps will take 20 minutes to arrive. So in the UI window you can follow progress + some other things. Maybe there should be random chances of delays for insured packages. And random chance for uninsured packages to be lost. The logistics window will show the status.
Maybe each player should be limited to 5 logistics jobs by default and then maybe a new skill that enables 1 more job for each level. Sort of how manufacturing and research jobs are also limited to around 10/11 per character. I for one am not a fan of the system cost index, but you could incorporate it into the cost of starting a logistics job i guess.