Thanks for the kind words for the hour or so I spent writing up the OP. I'd like to thank Fractal Softworks for making a game I can daydream about.
Thinking about the economic stuff I wrote about in the OP, I think I agree with you in that it's just too complex to create a full supply chain for everything. If things were simplified and abstracted, perhaps it would be possible. If there's anyone in all the game dev world I would want to do this sort of thing, it would be Fractal Softworks based on their superlative handling of the combat and ship customization portions of Starfarer. Looking forward to see what they come up with!
Psigun, I just registered for the forum to say that the reason I play computer games is for the dream of a game like you're describing.
The reason we're not going to see it in Starfarer any time soon, is that you're talking about a level of complexity that has not yet existed in any game ever. Consider how many programmers it takes to make even a relatively simple game like the Civilization series. I'm excited about Starfarer because it's moving in exactly the right direction, and I look forward to seeing how far it gets.