B) It should cost money, minerals, & fuel to do so, rather than generating such. In fact, it should cost more to have civilians move something for you than it would cost a government freighter to do so.
What's the justification for that? It's illogical. If the game is a simulation, then real-world, there's a reason why governments invest in private sectors and subsidise their growth: because they're much better at it than governments and they can do it a lot cheaper.
This doesn't mean that in Aurora, the player can sit back and have the civvies make it easy, because they're still going to have to plan where they need x resources, and set up their supply chains to make those resources get there when they need them.
Perhaps what this boils down to is the contracts system being slightly limited, if the civvies say to the player 'sure, we can set up a trade route from here to here,
but it's going to cost you. . . ' wouldn't you be happy with that? It would be nice to actually interact with them in some kind of basic way, even if it was purely asking them specifically to doing things, and for them to say 'nope, we can't do that' or 'yeah, here's our price. '
As a footnote to this discussion, if civvie industrial sector could set up mining ships it would make the game even better.