Fuel is redundant. If we became capable of interstellar travel, we would have to find a fuel source that doesnt need refueling, such as harvesting hydrogen or helium-3 compounds from space on the go.
As for oxygen, it wouldnt run out while in a core or computer, so no worries there. Also, you could have an oxygen module, similar to a docking module, that generates a well of oxygen, since there is no code for determining the inside of a ship or the outside, and you have to stay in the module\'s well of oxygen or hop into a core or computer. Terran planets would be the only ones with oxygen i would say, so they would be the only place you could walk about indefinitely without needing a module.
On the topic of food, the shops could sell synthetically produced MREs (meal ready to eat) and the player could start out with five. The MREs could refill like two food points or something, meaning the actual livestock being slaughtered would give you more food points, making players want to hunt animals or have on-board farms for larger ships and factions would need to stay with a Captial ship pilot for a food supply. Faction planets could easily be used to set up farms by adding a mating system similar to MC. Different animals would give different food point yields. Ice trolls on Icey planets would give like full health (cuz of all the fatty proteins) and pigs on Terran planets would give like four points or something. Idk about adding agriculture, but hunting and farming animals might be an interesting addition, especially if trying to make player economies where players trade goods.