Well, I suppose you are eagerly awaiting some of that in Windows as well.
Last I checked, "applications appearing like a single file" is quite OSX-specific. Windows uses installers instead, and linux its package managers -- package managers could install commercial applications, if anyone could ever agree on a common format.
Minor trivia -- the command-line tools for calibre are
unavailable on OSX, at least without manually making symlinks deep into the heart of the Schrödinger's file of an Application, after installation, because of OSX's Application bundle model. I've gotten around that, via an OSX port of my calibre-upgrade.sh here:
https://github.com/eli-schwartz/calibre-installer -- which breaks the Application-is-a-drag-and-drop-file model also.
On linux, applications go in `/usr/bin` and access their `/usr/lib`'s etc. and are easily available as a matter of course. Or install to /opt and symlink to /usr/bin, possible because of the package manager strategy.
On Windows, the MSI can add calibre's installation directory to the PATH.
Maybe there is something similar that can be done for OSX, I don't know. Apparently neither does Kovid.
Verify on application launch as opposed to signed installers?
That is orthogonal to your original complaint. As are sandboxes.
That relates to the security model, not the ability to publish an application that doesn't need recompilation for every trivial OS component update.
And some of that has been around for a while. SELinux, containerization, both are real today.
Frankly, they are only desperately urgent in a more commercial environment.
registry nonsense -- Windows, not linux?

Or do you mean that each file should be allowed to override its own mimetype and say which applications should open it, and each application should be allowed to, um, what?
Forgive me, I have no idea what OSX is doing, much less the motivation.