I know full well what warehouses in the real world are about and used for... there are many different operational circumstances and considerations but...
Bespoke warehouses are unnecessary in X4 due to the modular nature of stations, storage can be added to suit the station. For example: I have a number of ship yards (some with ship related production modules but not all) and ALL of them have 10+ million tonnes of storage for the resources/produced goods (some have >100 million tonnes of storage). My other smaller stations have varying smaller amounts of storage but most of them are not necessarily intended to be profit/production centres.
Trading in X4 is based on a very simple supply and demand model, not as simple as say Elite, Freelancer, and similar but it is still a VERY simple model when compared with real-world economy models. Trying to apply real world based economy model reasoning to X4 is fundamentally flawed and IMO ultimately wrong. Price fluctuations in the real world happen for MANY different reasons but ultimately ends-up being an upwards trend over time, just look at the cost-of-living metrics for the past 40+ years to see that (there are other factors too that prove this point). There are cases were older products (and designs) lose value too but the factors associated with that do not really apply in the context of X4's economy. Overall, what happens in the real-world can not be legitimately directly mapped on to a game like X4 - the economy model in such games is just too simplistic for such mappings in anything more than a VERY limited context - ware pricing and warehouses is not such a context.
As for no trading happening with factories that are not full, alot depends on stations but what you are trying to claim as fact is far from being universally true - ALOT depends on the precise universe state but I do have (and have always had) factories that are overproducing relative to demand and factories that are under producing relative to demand. There is nothing wrong with this being the case since the player has the means to affect both supply and demand through their own build projects.
I disagree with your proposed goals in the context of Vanilla X4, X4 is not just a trading-flight/fleet simulator - building is also a part of it, and arguably are the focus of the fundamental design. The current pricing models do allow for stations to operate at a loss and I see no good reason to exasperate the issue with what you are proposing. I disagree that making the pricing model more flexible would address anything of value - there is nothing stopping you from experimenting with your theories via mods though.
If you are having trouble making profit trading in X4 (even early on) then it is not entirely unexpected but the problem is not insurmountable... the motto of the X-series is Trade-Fight-Build-Think and while aspects of the game can seem challenging at times, normally with a bit of thought there are other options that allow you to beat the challenges. X4 (as with most X-Series games) is a title that really requires alot of time and patience BUT there are at least a few ways to make lots of money in the early game in order to get started with trading and building.
My point about trade routes is that they are generally speaking unnecessary and superfluous - comparable goals can be achieved by other means with a bit of thought.