AoE has chapters describing microprocessor operation, so those are the sections that will be of interest to you.
They directly explain how devices operate at their lowest level (machine instruction set).
Learning this, and learning what assemblers and compilers do, are the first step towards OS (well, kernel)
implementation. You'd also need to study OS theory. That covers the "how can i create my own operating system for a mobile device?"
question that you had.
For the "how can i communicate with a hardware?" question, you'd need to understand a variety of protocols. It should
probably come later, after you've got good microcontroller knowledge, and good C knowledge.
If you want to just do application programming, none of the above is essential.