You can build a star base (or mine I guess), with no commerce center and mining tools, and it should not be used as anything but a refueling stop. Add the commerce center and freighters could go there to pick up cargo. The challenge would be to find well positioned source of single resource (clouds work). If it has multiples, it should jettison other stuff if you keep using caslon for instance, to have an even supply of all kinds.
When it comes to long moves like you describe, it is in general a problem that the AI is very single minded when on a mission. If it has a move order it will move (until out of fuel I guess), when an emergency fuel order is picked up. But that should mean it forgets the move order.
Similarly, have a ship/fleet on refuel order and say 30% fuel. While docking the spaceport they are heading in to refuel at is attacked. The ships will keep docking for fuel, with energy/fuel in store, while the spaceport is attacked.
I doubt it is useful for moves, but you have the "move to leader" behavior of fleets. If the fleet leader sits at the destination, you can tell individual ships (or multi select them) to refuel. They will refuel, and when done so, park outside the refueling stop and think "what to do?" and figure out it should move to leader.
Very useful when a couple of ships are out of fuel, when doing invasions, when sending single fleet members to investigate marked locations or pick up alien ships, when single fleet members are out of fuel, or when sending 2-3 fleet members to attack each of the enemy mines in the area.
As long as the fleet leader sits around, they will all end up there unless killed/disabled.