A second big point would be to realize that everything is part of a system. Nothing exists in a vacuum. As part of science, we using modelling which assumes vacuums or other inaccuracies to make reasoning possible. Think of the "spherical cow".[2] These simplifications make reasoning easier, but have hard limits that must be recognized. Quantum mechanics are true at a tiny scale, and relativity is true at a macro scale, but we do not have a well tested unifying theory (string theory and such are possible explanations).[3] Physicists are still asking why to understand.
As for growing these skills, that's tricky. Arthur Conon Doyale was a physician[4]; he studied an incredibly wide range of topics to inform himself. Knowledge is required, and unfortunately, the way to knowledge is through experience. The story of the master ship builder who looks for an hour, and taps once to fix a broken ship is true - you've identified it yourself. The process of gaining experience is one that people would love to hack, but unfortunately, in real life, there are no silver bullets. Your best "hack" here is probably meditation, though it sounds strange. The other "hack" might be one of "always saying yes" like in the Jim Carrey movie "Yes Man."[5] You get a lot of experience rather quickly always saying yes, but it seems rather dangerous too. Reading a lot helps: HN is a great source of diverse information which is nice.
One of, if not the biggest, problem with Capitalistic commodification of labor is the reduction of human capability. Briefly, we see this in a few places: one is the devaluation of experience, and the other is the preference for credentials over skills.
Experience allows humans to grow - a junior dev can, in fact, become a senior dev. Most commodities cannot do this: your tier 2 generic branded Orange Juice can never improve to become a tier 1 Tropicana OJ. So, experience isn't valuable to some people who treat humans like commodities.
The credentials come into play because they can be used, theoretically and incorrectly, to identify you as Tier 1 Tropicana or Tier 2 generic brand OJ.
Capitalism baby.
[1] https://en.wikipedia.org/wiki/Five_whys
[2] https://en.wikipedia.org/wiki/Spherical_cow
[3] https://en.wikipedia.org/wiki/Fundamental_interaction