What's the goto for step-by-step instructions to edit the code directly?
Assuming that you have already downloaded the source, the files you might wanna look into are config.h, your header file (kb.h when downloading from kbfirmware.com) and the keymaps.
The real deal is in the header file as you can add multiple layout supports which are then implemented by the keymap files.
A straightforward example of that is the
code for the XMMX and the Toad which share the same matrix and therefore use the same firmware. You can find more info about those in my signature.
what are the benefits of getting into the weeds of QMK that kbfirmware doesn't cover?
Basically implementing other features. For example, if you have shift registers in your keyboard, you need a custom matrix.c file as in the
Pegasus Hoof.