While Vic 3 is the most complicated of their games so far, it's still a grand strategy, not a reality simulator. All those are thought shortcuts, even the last one which is particularly idealist thought shortcut.
While I do think that PDX are more concerned with building an internally consistent simulation than one that is consistent with reality some of these complaints maybe just lack imagination.
Maybe you can’t stockpile goods because manufacturers want to sell them to willing buyers, they go bad, or they go out of style. Your textile producers may be selling more than the immediate production need to clothiers, who then stockpile some. It’s not implemented in the game but if you could stockpile resources - while cool - it would introduce all sorts of balance issues and require new mechanics like perishability.
The train thing too…they probably don’t need to replace every train weekly, but your production represents parts and design work too.
Overall I still think Vicky 3 will be incredible…in a couple more years, like Stellaris was.
They've stated before that the economy is meant to be understood as an abstraction, the things you're observing on the market are not actual goods moving between producer and consumer, they are buy and sell orders, functionally indications of capacity to produce and demand to use a good. And once the imbalance reaches a certain proportion it does negatively affect things, shortages cut throughput on the entire production chain affected.
I think you can effectively simulate stockpiling using subsidies, using government funds to, for example, keep your arms industries large enough to supply them when they are fully mobilized even in peacetime, as an example.
The probable reason as to why you can't stockpile goods is the same reason money became scarce at the endgame in vic2: the AI hoards it.
You think it's bad that other countries don't extract the basic resources your economy needs? Now imagine they are stockpilling it too...
Expect communism to get heavily nerfed in every single balance path. Paradox games' fanbase is largely reactionary, and they love to complain. HOI4 had a similar issue where the USSR was nerfed and Nazi Germany was buffed practically every single patch. I expect Vic3 will have similar issues.
Just like the US forces in armed forces wargames.
Which is funny since Germany is always ahistorically strong just to be able to win WW2, even though they couldn't defeat the soviets ever.
BUT THE PANTHERS! THE TIGERS! THE WUNDERWAFFEN 
I think the IG one is kind of annoying, though I expect it will probably be updated within a year or so. I think stockpiling would be a performance nightmare, though I could be wrong.
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