Your fifth point isn't really single level store, as you say,
programmers and thus apps don't care, it is the OS architecture. The
i/OS architecture could be implemented on another file system,
they are "just" objects. The Amiga (Intuition) implemented a similar
object oriented OS over a "conventional" file system back in the 80's.
IMO a superior OS that died because of the lack of advertising/inertia
As to your forth point, There are several companies that would not exist
if Windows/*NIX OSs had to have the level of "native" security that
single level store requires of i/OS. Putting the security overhead in
the guts of the kernel and OS is much more efficient that putting it on
top of the OS.