No market ever works like that.
Yes, they do. Real-world stock and commodity markets display exactly this behaviour if you're selling (or buying) large quantities. (Except that the real-world equivalent "bulk tax" mostly depends on how much you're selling, not how much they think you have, which I've already said is the problem with how they've done it)
Imagine a set of "buy" orders waiting in the market - one person wants an Opal and is willing to pay 400k for it, another wants one at 700k, another really wants one and is willing to pay a million.
In a real market, if you come in to that situation with a hundred opals, the first buyer gets the first one at a million, and then you work your way down the list, getting less per opal as you go. You don't get to sell a hundred to the first buyer (who only wants one), and you don't get to sell the other 99 to the other buyers at a million each just because one person was willing to pay that for one of them.
In Elite Dangerous there's a simplification in that the buy orders (and the sell orders, if you're not dealing with mining-only goods) always neatly line up a tonne at a time in a linear fashion ... whereas in real life they'd be more blocky and uneven, and things like futures contracts and derivatives would try to even out some of that ... but it's not unreasonable for a game that's not really trying to be Spreadsheets and Stockbrokers.
Because people with huge ships make better money? Why shouldn't they? They invested time and money in that ship and then spent hours and hours filling it up. Why shouldn't they receive a better return for the extra effort?
This I agree with, and I'd be happy to see the bulk tax just go. Because of the exponential cost curves in Elite Dangerous, big ships already have a much higher "time to pay for themselves" than small ones, so it doesn't really need anything else.
But all that implies the market actually responds to supply, which as far as I can tell it doesn't.
The market responds pretty strongly to supply.
Each market has a baseline demand level for its imported goods (bigger markets are higher baseline, and therefore don't respond as quickly). If the actual demand is 100% of the baseline, you get full price.
As goods are sold to the market, actual demand reduces, and so does the price. The effect of this varies between goods, but at "minimal demand" getting about 40% of the maximum price is typical.
Actual demand will then recover over time back towards the baseline - representing the goods being used up within the economy. The rate this happens depends on the good - in general, the more fundamental cheaper goods get used up quicker, and the expensive luxuries get used up slower.
BGS states - representing underlying economic and political pressures - can adjust this, either by introducing new buyers, or making the existing ones take more or less of the good, or by shutting down so much of the economy that no-one wants to buy right now. This can both affect the short-term price (e.g. in Pirate Attack lots of people will buy weapons, pushing the price up temporarily) and what the demand looks like after the state is over (if the economy goes from wanting 100t a day for equilibrium to wanting 300t a day, but only 100t a day are being brough in, then when this goes back to 100t a day the demand level will be higher up)
This is true for pretty much every good already - the only "micromanagement" is that it now also applies to gems, which for some reason it didn't previously (and if it hadn't been for people really liking always being able to get full price for gems regardless of supply, could have gone in as a quiet bug fix and hardly anyone would have noticed).
So ... why haven't you noticed this?
1) It's only recently been enabled for the lucrative mined goods, and A-B trading hasn't been a particularly high-paying option for a very long time, so no-one has really focused on how it's already been working for (say) Non-Lethal Weapons or Coffee.
2) For most (not mining-only) trade goods (Palladium the only real exception, though anything above about 6000 credits average the effects are visible) the quantities demanded by stations are so large (and regenerate so quickly) that there are nowhere near enough traders in the game to seriously make a dent in the supply or demand levels, so they spend most of their time at full price.
Outside of a few niche cases, CGs are the only thing which can get enough people hauling the same thing at the same time in the same region to do anything noticeable to supply levels. (And CGs have demand pinned artifically high, of course, because when they didn't - years ago - the mass sales would very rapidly mean everyone was making a loss on their trades as the demand price plummeted)
3) Because of 1 and 2 the famous third party tools don't bother tracking prices over time or how they respond to demand, so neither they nor the in-game tools provide the graphs of historical price/supply/demand that would make this all obvious.
Essentially, the market is
far too large for the player base, so player actions rarely have a noticeable effect on it. Making the market smaller would make it more exciting, prices more unpredictable, and actual knowledge of how it worked more valuable ... or, as it's called nowadays, "nerfed".