Wikipedia says that Embedded Controllers [1] are microcontrollers (like an Arduino!) that control everything the OS doesn't. It looks like these slides describe how to program said microcontrollers.

[1]: https://en.wikipedia.org/wiki/Embedded_controller

I do not think this slide deck is really trying to get you to try to frankenstein something out of the board but more that there is a well established microcontroller they are using in the chromebook with a well-developed software platform to run on it. If anything the 'franken' part just comes from using the Chromium OS code and less the actually common microcontrollers.

Blinking leds is one thing, hiding encryption store is another.

Remember a story of GCHQ going over Guardians Macbook with a dremel and destroying every single chip capale of storing bits?