Alright, glancing through your files for econ generation. You start with a randomized base of sectors based on some market stereotypes, and then you trim out the extremes to balance it out.
Balance here is based upon expected supply and demand of the overall system of planets.
Some interesting aspects about this.
1: Enemies don't ship to each-other as I understand it. This means if the supply for a product is on one side of a rivalry, and not the other, then there will be a price imbalance that occurs.
2: As I understand it, shipping isn't really based upon demand in a way that really scales. Because actors in your economy are not profit-motivated, imbalanced continue and can keep increasing. There is something of a limit to this, but the market doesn't really ever try to 'correct' itself.
3: Likewise, as I understand it, trade doesn't occur as much over long distances, so you can get a similar cut-off from a sector that happens to be very far away.
Edit: That said, I have spent quite some time trying to reproduce this problem, and looking at the way the economy flows. Best I can tell there is far too *much* production, not too little. I have trouble finding the basic economic imbalances that lead to any profit at all, and I have made a handful of worlds to test this. As it stands now, I contend you basically have killed merchants because of the way the economy currently functions. Admittedly, they were quite easy in vanilla, but this extreme is a bit of a problem.
If you are to try to adjust for this, you need smuggled goods to transfer when market imbalance gets very high, or at least some sort of response here. Right now these effects are what you use to have pockets where a player can profit as a merchant in the normal game. Its why you almost always start with a ton of money you can make off of short-range supply trading in the base game. With tarrifs are they are, its a very real need.
If you want to correct this, you need some sort of reflexive economic response to high/low prices. Whether that is building a new economic trait and tearing an old one down, or triggering new trade routes.