<ahem>
This is (kind of) my fault, OP.
I told Alex, "keep the economy really simple" ... er, 3+ years ago.
Why? Because I'd had experience with (and re-coded, at one point) the Mount and Blade economy, that tries to simulate a lot of things pretty directly. Like, for example, local farmers bring grain to a local city and trade it; it gets turned into bread.
This works OK-ish when it's that simple, but... when you start adding a lot of resources and dependencies and then let the player directly manipulate the world's supply chains, it gets super-duper broken really easily, unlike real-world economies.
It sucked and was easily manipulated by players in un-fun ways, and it's almost impossible to fix that issue, frankly.
Really!
The problem with economic sims that actually attempt anything like real fidelity and include a lot of goods and services is that they really require a lot of AI-like gamecode trying to make it work out or weird rules or odd fiats (like, say, Mount and Blade's "tax penalty" where the player literally got less and less tax money for each new Fief they acquired- a pure hack to keep players from ever being able to win the game in a reasonable timeframe).
Problem is, that kind of code's bloody expensive per calculation run and it scales exponentially, not linearly, with additional markets to consider. Which is why the Mount and Blade mega-mods that add lots of cities but don't fix the economy mainly run pretty sloooooowly, even on modern PCs.
Moreover, it doesn't add fun. This isn't a game about being a masterful economics wizard. This is a game where we build our ride-or-die fleet of sci-fi hotrods and blow everybody away, with pyrotechnics. Trying to also simulate a realistic economy and interactions is kind of like strapping a nuclear reactor onto a LED... sure, it can be done, and Alex sure tried, despite my advice... but it was largely a waste of time and energy.
Alex wrote two major iterations with complex economics under the hood. If you've bought the game, you can even play these earlier iterations; all of the older Alphas are available on the website. I'd suggest trying them out to see why things got simplified.
But, if you're willing to hear out a total stranger on the Internet... neither system worked well. They had all of the problems I'd predicted, no real benefits to gameplay, and the UIs were so complex that I had friends try the game out and walk away muttering about how Byzantine it was. They just wanted to do some straightforward trade runs and make a profit, but it was well-nigh impossible to figure out how, exactly. Not good.
If you don't wanna take my word for it, download 0.6 / 0.7 and see for yourself. Try, for example, cornering the market for Organics, by deliberately destabilizing all Organics production in the Sector other than yours (or in 0.6, just build out Organics in ideal locations... over and over).
So, did it add Fun? Nope. Just easy money for the player and a Sector whose overall economy thrashes and crashes, because disabling things was easy. Also, like Mount and Blade, there were problems all over the place with initial conditions of supply / demand that spiraled if you played a few game-years in. No dynamism and no really sophisticated AI make for treacherous conditions to build economic sims.
Now we're here, where it looks complex on the surface, but is actually quite simple, as you've partially discovered. I'd vote that it's hugely better, too, because it's not such a mess and it's easy for newbies to understand while having some depth.
The player's economy is largely untied from the global; the rules are straightforward and creating synergies is easy, once you understand the rules. The trade fleets aren't dealing in "real goods"; they're actually mainly window-dressing. The real economy is the relationships you create between your worlds.
So, it provides something to do, it looks like an economy and for all practical purposes, acts like one, except for the complex simulation bits and connection to the other empires, which really wasn't adding anything fun. And, unlike the two earlier systems, it performs well.
Sorry if you want to play Space Accountant 2000; this just isn't it. But, frankly, if that's what's actually bothering you... step back, play what's actually here. The main game isn't economics; it's not even about money, really; that's a minor obstacle at worst. You cannot solve your main problems with cash, either, which I think is how it ought to feel.