Governments run the logistics
Every NPC logistics carrier is now owned by a public entity — city operators by their municipal government, national flagships by the national treasury — and the government can run them.
The NPC shipping companies are no longer ownerless background infrastructure — they belong to the public.
Public ownership. Each city's logistics operator is now owned by that city's municipal government, and each country's flagship carrier by the national treasury. Their shipping revenue flows into the public purse it serves.
Government control. From the Logistics tab of a government you control, you can run its carrier — see its deliveries, on-time record, fuel, and depots, and set its shipping rates. Cut rates to make trade cheap across your territory, or raise them to fill the treasury. (Fuelling and fleet expansion controls follow.)
Carriers behave exactly as before for everyone else — this only changes who owns them and who can steer them.