Maybe it's just me, but I don't see the flows to be where the goods go, but rather where the profits end up. This is the age of Mercantilism after all, when trade was seen as zero-sum and self-sufficiency was the ultimate goal.
Spice trade with Mamluks causing a silver shortage, for example, could be represented by them clamping down on profits leaving their primary trade node towards Venice's. Something like the Opium Wars (which caused a similar "so much money flowing the wrong way it started a silver shortage) could be represented by China holding nearly all the Trade Power in the Asia trade nodes, until Great Britan won wars that forced them to transfer trade power and give them trade centers.
In that way, the real flaw is that there are actual begin points and end points; There really should be neither, and any nation could see all their production profits get siphoned off by someone else downstream if they're outplayed, or find themselves the trading mecca for the world if they play their cards right.
"where the profits end up" as if only one side profits. Again, if trade is in any way fair (not counting looting situations like the Americas), both sides profit. Mamluks and Venice both made serious money from their trade. Mamluks got silver, Venetians got pepper which they traded inland for goods, favours, ships, or everyone else's silver. Trade, by its nature, should be good for everyone.
You mention China: that doesn't mirror the real-world situation, where the British were still making amazing money, but wanted more. After opening up trade, the Chinese still kept making huge profits, just a bit less because now they were forced to accept terms favourable to the Europeans. But, profits didn't just vanish.
Its just.... not how trade works. It's how looting works, and looting should only take place with vastly unequal power.
I mean, many situations in eu4 are not and are not intended to be direct historical simulation. The speed at which certain countries were conquered, for instance. Ottomans take around least 3-4 wars to absorb the Mamluks in eu4, but took up deep a decade in real life, because the Mamluks surrendered in exchange for concessions. Thus isn't simulated because eu4 doesn't work that way.
So,no economic system will be perfect, either. But what I'd love to see is a system where trade goes both ways, and profits aren't sucked away unless there's a huge power differential. Where trade steering does matter is when we determine what route goods take between countries. Say, between Europe and China, do they go around India via Egypt (thus profiting whoever controls Egypt) or around Africa (thus profiting whoever controls the ivory coast)? Or maybe they go overland north of the Himalayas, benefiting the tribes.
I mean, that kind of trade steering was one of the key drivers of the era. It's why the age of exploration began at all: the Ottomans blocked the silk road, so they needed another route to the Indies. Portugal went around Africa, Columbus drastically underestimated the size of the globe and went west, only the continent of America saving him and his crew from starvation.
The current system does do that (but only if you conquer a bunch along the way, Portugal's powerful trading empire would be laughably pathetic in eu4, since they don't have enough power in each node, since their ships can't just take it all back to Sevilla). We just need to make trade more like trade - ie, mutually beneficial - and less like a zero-sum game.
