Some docs improvements (#15845)

* docs: clarify in "Keymap Overview" what LAYOUT is and isn't

It is not strictly necessary to use LAYOUT macros in keyboard.c, but it
is a convenient abstraction of hardware internals, allowing focus on the
physical keyboard layout.

From the C source point of view LAYOUT is macro with a parameter list,
which expands to a array of rows that each is an array with a keyboard
scancode for each column. A macro parameter list is not an array, and
even less a single array.

Perhaps no big deal, but also no reason to give incorrect hints.

* docs: update "Understanding QMK's Code" to current code structure introduced in 96e2b13d1de

This part of the documentation was no longer correct. I tried updating
it, mainly copy editing and using github links to latest release.

This is not trying to fix all problems, but just trying to fix some
problems while reusing much of the old phrases and structure.

* Update docs to use "qmk format-python"

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