Some suggestions for the civilians shipping orders mechanic.
1. Allow the player to specify supply and demand of minerals. This should preferably be in multiple of 1 thousand minerals to make it easier to set up.
2. Allow supply orders for installations that don't exist yet. When checking for supply to assign to a civilian check if that installation exists and then reserve it instead of failing to pickup when it doesn't exist. Current functionality makes it necessary to constantly update the supply when new installations are built for example when building terraforming installations at Earth would be nice to simply set supply and let the civilians check if it exists yet.
3. Allow civilian shipping of maintenance supplies and fuel (with the required new civilian designs). This will make it easier to manage outposts.
Again, these largely amount to "remove any remaining need for government-owned shipping" and I, for one, would like to see shipping lines move in other direction -- that of becoming less useful.
I don't see why we could eventually get both.
First of the civilian economy should actually consume Trans-Newtonian elements... either by mining them or buying them from the government. Lack of minerals could then have reduced production capacities and the like. Now.. this could be solved through the civilian trade system in some form.
Now... civilian shipping lines should require both fuel and minerals to operate, like government ships. There should be no free rides anywhere... fuel in particular needs to be created even for the civilian fleets.
You as the head of the government could then dictate in what field the civilians are allowed to operate... so you could ban civilians from mining at all, build fuel harvesters or just ban certain systems. Although there can be consequences by doing that... if you restrict them too much their income might go down so they can't maintain their fleets properly.
Now... operating government owned commercial ships will still be highly useful even if there is a civilian fleet doing some of the work. You as a player also can restrict the civilian fleet where it can operate which will impact their economy and the amount of ship they can maintain and build.
I also think that both Commercial and Civilian ship should cost an amount of Wealth each year in a maintenance fee... it could be something like 1/20 the build cost of the ship in a yearly cost. This would represent crew salaries and general maintenance of the ships.