There are two books that taught me how systems work.

- One system in isolation - Operating Systems: Three Easy Pieces. Covers persistence, virtualisation and concurrency. This book is available for free at https://pages.cs.wisc.edu/~remzi/OSTEP/

- Multiple systems, and how data flows through them - Designing Data Intensive Applications. Covers the low level details of how databases persist data to disk and how multiple nodes coordinate with each other. If you’ve heard of the “CAP theorem”, this is the source to learn it from. Worth every penny.

More on why these two books are worth reading at https://teachyourselfcs.com