Instead of Exclude (qualifier) for the logistics list, it might be better to have Include (qualifier). ie. Include (Armed), (FAC), (Fighters), (Tanker), (Supply), (Collier), (Freighter), (Civilian), (In Shipyard), and just tick all the boxes at the start of the game so the entire navy is on the list.
Civilian would be the catch all for terraformers, fuel harvesters and any other ships not otherwise on the list. And yes, if a ship is a supply, fuel and ordnance support ship that does mean that they can qualify for the list on all of them.