> This is typically NBD (well, no huge deal), but it deserves mention. Managing remnant traces of .app files requires either manually navigating the OS and deleting files, or using 3rd party apps.

Apple has moved to solve this problem in iOS (and the Mac App Store) by maintaining per-app metadata directories. I think this is ideal, and it's not necessary to attach it to the app store model.

> More importantly, when I use OSX, I most certainly am also variously using brew & make to install various pieces of software not packaged as .app binaries.

Yes, UNIX software.

> Lastly, even assuming all binaries that could possibly be executed on a given system are packaged as .app file (equivalents), I frankly wouldn't mind having a package manager available to install (copy), manage, organize & remove my binaries (including support files).

That's what the file system is on a system that manages applications sanely.