After reading the article, this comment and the comment thread further down on pnpm[1], it feels to me like the NPM team are doing everyone a disservice by ignoring the inefficiencies in the packaging system. It may not be deliberate or malicious but they could easily have provided better solutions than the one proposed in the article which, in my opinion is a band-aid solution at best. The real fix would be to implement what you mention here: local registry and caching, and/or symlinking a la pnpm.

[1] https://news.ycombinator.com/item?id=42841658