I think it is important to keep in mind that in Aurora, the cost of things is usually in terms of TNEs, which we can generally assume are not the entire actual building requirement for an entity. The cost of things in good old concrete, steel, etc. is not included and at the scale of the game we can assume these are generally a negligible economic cost compared to the rare TNEs. A manual mine for instance costs 120 corundium (240 shipping tons) yet takes 25,000 tons to ship as cargo, over 99% of that facility is presumably made out of traditional materials. Similar for ground units, a typical early-game medium tank requires just under 5 vendarite to construct but requires 62 tons of transport capacity, and you are not convincing me that a medium tank is 5 tons of tank and 57 tons of supplies.
In the same way I think we can abstract fuel, mineral, etc. storage as being cheaply-built warehouses, tanks, etc. and not the hardened high-tech TNE-enabled construction we use for spaceship or military hardware. As Garfunkel points out, physical storage area is decidedly not an issue, even a small 100 km diameter has some 30,000 km^2 of surface area to work with, if you assume fairly short 10m height storage facilities and that 1 ton = 14 m^3 as Steve has used unofficially elsewhere this comes out to some 22 trillion tons of storage on that small rock, which is far more than the starting facilities on Earth even in a 12b pop start.
I also want to reiterate that besides adding more logistics micro (and not the good kind IMO as there is not really much decision making involved in "this planet is full, we need to dump everything on the nearest moon"), this really would not add as much strategic depth as people are imagining because Aurora is (until v2.0 and the new spoiler race) dominated by jump point network topography and JP defense, and come v2.0 there will be more than enough strategic depth in rear-areas defense for those who want it without resorting to adding new micro-heavy mechanics.