This is starting to smell like a system on top of a system to fix something that could be fixed in the system. Kind-of like implementing a filesystem on top op a filesystem... or putting a database on a filesystem to run another filesystem inside the database, or using a webbrowser as a runtime instead of an operating system.
The whole notion of containers is basically this. That's why I am not sure why not just fix the OS. If there's anything to fix in the first place.
I think there's interesting ideas of environments in other operating systems, but I'm not seeing how you'd make things better by flattening containers into the OS, per se.