Their official way to configure the system file is creating a overlay image that contains all necessary change to root file system and load that into system. This way may be more complex for a developer to do, but is much safer to end users. Because you aren't changing anything, you only add. And fxxk up only means you need to unload the newly added image.
It'd be easier to use if it can automatically do it for you though. Something like, enter a special env, install packages, leave and it automatically pop up an image for you would be nice.
I think this is quite similar to docker image layers except it is composable
