Understanding "arduino.h" and "arduino.cpp"

the frequency by default it's 490Hz, phase-corrected mode, interrupt on top disabled. BUT if you would like to change it, let's start to study".

I don't know if I've ever seen that level of documentation for a piece of software that wasn't explicitly designed as an educational example. It tends to lead to a rabbit hole of details that really aren't that useful or interesting. (For example, for your PWM example, it would be really uncommon to say "I disabled interrupts", instead documenting cases where you turned interrupts on. And the 6 PWM outputs of an Uno are distributed across 3 different timers, each of which is configure slightly DIFFERENTLY (timer0 also generates the millis() interrupt. Timer1 is a 16bit timer...) And of course it's all likely to be completely different on a different CPU (Nano Every has different timers; Due has a special PWM peripheral.
I think your question is sort-of like "I want to learn all about physics without having to do math." Eventually, if you want to learn about the Arduino PWM modes, you MUST learn about the chip timer details.