I'm new too. Just wanted to say that trade is confusing at first but makes perfect sense after you get used to it.
There's a lot of frustration because lots of the mechanics are fairly situationnal, but the game is good at making those situationnal pro/con relevant at some point. It isn't very clear when starting out "how and why" stuff works the way it works.
Usually if something looks like a fake choice, do it again and again and you will encounter a situation where the choice suddenly makes perfect sense.
It's like the game as a "base" state where all profit opportunities are closed and sometimes it open a window that enable you to profit from a situation for a given, usually short, period of time. This obviously will pay more if you use the black market. Those situations arises from the simulation, conflicts, etc.
The "procurement missions" are a newbie friendly way to highlight and secure an opportunity and a (generous) margin for a given situation. But in many cases, even without a procurement mission those opportunities can exist.
Since all stations/colony orbit their stars, and jump points are limited, lots of convoy must go through the orbits to reach the JPs. This means that in some cases , those convoys will cross other worlds, potentially patrolled by hostiles forces, which will destroy them and create loss of accessibility, loss of import/export and eventually shortages. And it can spread to colonies that rely on those import/export. This is the "engine" that creates "windows of opportunities" for the player. (there also are patrols, raids, hostilities, etc). Pirate and Luddic pathers gives guarantees about the instability : either the system isn't very strong and pirate raids/activity will kill convoys and destabilize colonies, or it is very strong with lots of infrastructures and productions, but then I think the luddic pathers will create shortages with inside jobs to destabilize it.
The transponder thing is smarter than it looks : some mission requires you to dock with the transponder "off" (I.E. smuggling stuff to the local underworld) - and in some cases, this is very difficult to do due to patrols, or takes lots of IG days to slip past said patrols which makes the mission deadline more relevant.
Some colony are super easy to smuggle from/to, some are very complicated or nearly impossible.
Tied in with the procurement missions, if you need 300 recreationnal drugs and you have 10 days left, you might not have the time to "sneak in" (especially in systems with sensors arrays that crushes your ability to do so), and will be forced to buy from a black market while you are docked in with transponder on, which will tag you as a smuggler and will push patrol to scan you, running the risk of losing rep, losing the cargo, and failing the mission.. And worse, if the smuggling procurement requires you to have the transponder off when docking, but the target colony is nearly impossible to dock with transponder off, you must consider destroying any sensor array first, then consider how to lure away patrols, etc. This goes in the same direction : deadline suddenly doesn't feel that comfortable at all anymore.
And if you do enough of those missions, you will build up "suspicion" on yourself that will complicate subsequents runs : the same "source" of goods will becomes way more difficult to use because you might still be tagged as a smuggler by a colony and a fast picket might scan you at a jump point or at another colony's port in the same system, even a few days after.
So you end up thinking about storing some of the goods that are complicated to get (I.E. smuggling small quantities to keep suspicion to none or to minimal each time you get the chance to do so), but then you realize it can be expensive becauses of the storage fee, which push you towards considering establishing your own colony to store and trade....and that makes "reputation" with other factions very relevant, as well as shortages and surplus, which ties back to the open/black market thing
Without that kind of stuff, the trade and events would be uneventful and boring. There would be no decision to take at all and no consequences when taking "shortcuts". It also allow the game to reward the player for learning the stellar systems, patrol routes, convoy routes, hiding in asteroids belts, using transverse jump, etc. And still, sometimes you get caught because the planets were aligned and bad luck slaps you in the face. It creates some kind of narratives which is the purpose of that kind of "living" universe.