This is very cool! I like the idea of atomic distros although I haven't really gotten into them much, if you keep on working on this project I might join it.
Question: I'm a bit confused about the package management system you talked about. Flatpaks for user level packages? What about the official arch repo and the AUR? I know other atomic distro's don't really work with traditional package managers, what does this mean for Pu-239? If there's no AUR then there is no Arch Linux at least for me.
Also that name could probably do with some work lol. Maybe work on a shorthand way of spelling it and a better way to pronounce it? I'm not sure.