You have placed your harvesters under a general administrative command, you need to change the type to an INDustrial administrative command so that you get the 25% of the commander's mining stat bonus to mining and the 10% of his logistics stat to refueling. What are the stats of the commander you have assigned to " Fuel Harvester Command"?
Admin commands are at least system wide and with additional naval headquarters the command radius increases to adjacent systems, so having all of the fuel harvesters in the system, even if they are at different locations, is the way things are intended to work. You should have a fleet for each location, as this makes it easier to send tankers, or tow additional harvesters to a given location.
The advantage of having individual commanders on each harvester is that the commanders mining bonus increases the mining rate, and the commanders logistics bonus increases the fuel transfer rate, auto assign will put commanders with the correct stats on the harvesters, but you can manually add junior commanders without the correct stats, as they are more likely to pick up the stats (on-the-job training) if they are in a command position than if they are unassigned.
Also, all of your admin commands are general. Cargo Fleet should be LOGistics, Exploration should be SURvey, Logistics and Construction should be split with freighters, tankers, and colony ships in one or more LOGistics commands and orbital miners, salvagers, and jump point stabilization in their own INDustrial commands. I usually put the battle fleet under either a NAVal admin command or PATrol admin command.
Please the links above to read up on the proper use of administrative commands.
