Ok, let us try to separate the two discussions here.
As a GAMER, I can understand how nice it would be to be able to just transfer fuel from any ship to any ship, have fuel transfering systems even on small ships and the like.
But since Aurora tries for pseudo-realism...
1) These ships are far more complex than we can imagine, since they are much more technologically advanced than us. These are not gasoline burning engines. Remember, to the caveman a simple phone would be "Incomprehensible magic". They are surely more complex than nuclear reactors, so I really HAVE to assume you can't just strap some tube between two ships and transfer some gasoline-equivalent fuel.
2) It would be one thing if we were talking of immobile ships in space. But here, we're talking of transfering fuel between two ships half-submerged into another dimension, moving at trans-newtonian speed in some sort of pseudo-dimensional bubble. And you want to connect them and transfer fuel. Once again, I have to suppose that this require some exceptionally sturdy and specialized equipment. And most assuredly, not throwing barrels of fuel from one ship to another at trans-newtonian speed...
That aside, I think the point is rather moot. I will say it again, it seems to me that Steve wants to create an additional, logistical layer for the game. One where you have to deploy tankers and refueling stations across your territory and defend them, for example. If every ship could just transfer fuel, then all of that would be pointless. And Steve would have not coded this change.