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An example of this is food production, more often than not cities will spread towards humid soil (that or the city is already flooded) so its possible to move all food production where its in mk3 depo distance of pumps with the only input being nitrogen. Build carbon production within or next to the food module so it can be transferred via depo rather than train.
There is a lot of potential for different storage since a planet is a closed system. So in some sense its all storage, just don't make too much terrible stuff and it will be fine...
Some more ideas for endgame transport could be teleporters, dropships/really big drones that can carry more things, father, faster. Similar to what you said about mining on moons, but just make a space elevator that sends stuff up and then it comes down somewhere else-this is essentially the same thing as the telelporter, but I guess they could be separate things
. I would say the teleporter would be more high tech, so if and when the devs add more materials, it can be a very hard thing to make, or it takes along time to charge or something. Maybe there would only be enough for make a couple of them per planet, so you would still need large mining and transport networks, but you wouldn't need to transport stuff cross-planet.