The one aspect of the economy that really challenges my suspension of disbelief is earning revenue on total production - upkeep, rather than net production--it seems weird that if I have a refinery and a mine producing just enough to feed the mine that I still get the same profit from ore exports that I would if I did not have the refinery. Reduced upkeep for in-faction sourcing provides an incentive for vertical integration but makes that even more implausible because the player explicitly double-profits from intermediate good production.
I would consider calculating the player factions' net imports/exports of each good and adding expenses/income based on those (probably incentivizing vertical integration with a spread between import/export prices)--it seems a lot more intuitive, although it could make it too hard to make a financially-viable colony at first.
TLDR; Starsector's abstract treatment of supply/demand is in many ways more realistic than economy simulators that count units of production.
The weird thing about the economy is that, while it is heavily abstracted, in this manner it is a lot more life like than most 'economy' simulator type games. The idea that industry has some fixed output production level that it makes at all times is at odds with how real world industry works. A rigid supply base operating at 100% capacity is efficient, but very bad.
As an example, take mining or factory output. In almost all cases, the amount being output is the amount that the mine or factory can secure a buyer for, up to a maximum set by the infrastructure present. When demand is especially high workers are called in to work overtime (or more are hired), the plant is run 24 hours a day, etc. But when demand is lower, the opposite happens. When demand is consistently high, the company may invest in infrastructure to increase their maximum possible output, but this carries a large risk as if demand lowers again than the money is 'wasted'.
The demand for components in one industry is almost never static, but goes through upswings and downswings. And if your suppliers are running at flat out 100% capacity, then they cannot expand production in short order to fulfill unexpected needs. So in practice, suppliers will have some amount of excess capacity in a good functioning system. Not only that, but in order to secure themselves against unexpected crises in the supply chain, consuming companies will spread their contracts around to different suppliers (and also if you have multiple competing suppliers, they will offer you lower prices). Those suppliers of course lose some money on excess capacity so will take outside contracts if they can find them.
This comes back around to the SS setting: say you have a heavy industry requiring 4 metals. This is saying that it needs suppliers that can operate at 10^4 scale, whatever that may be. Those suppliers though aren't going to be giving 100% of their output to the industry though - they will have excess capacity to deal with spikes in demand, and when those spikes aren't present they will export to others, if they can get buyers (accessibility).
Here's an example from recent real world: Apple tried to move the domestic assembly of one of their computers from China to Texas a decade or so back. They ran into a problem when they suddenly needed an order of 16000 custom made screws - the local machine shop companies in Texas could not fill a sudden order of that size, so Apple's operations were disrupted until they could secure a supply. This is an example where the local supply size could
usually fulfill demand of the company, but was not of sufficient scale to fulfill a spike. In SS terms, this would be a industry requiring say 4 units of something, but only having a supply of 3: it still has output, just limited by problems. Meanwhile, the machine shops in Texas were still exporting goods to others, despite not being able to fill that large spike order - in SS, the 3 output mining or whatever is still making money.