Does anyone have any good guides to trying to understand how this OS is custom built and being able to modify things. I am used to not-docker and being able to modify files/packages directly on linux and unix.
Then don’t install Home Assistant OS. Use one of the other install methods, if you modify HAOS it will likely get marked unhealthy and you won’t be able to update.
HAOS is designed as a turnkey solution - if you want to fiddle then docker is probably your go.