What happens when the user wants to install software that's not in one of the install's default repositories? The web page walks them through adding another repository URL to their package manager GUI [which is YA of a dozen]?

Then they're in roughly the same situation as a Mac OS X user installing new software, which I agree is a pretty crappy situation to be in. But, we somehow muddle through, and if the software does have an apt or yum repository, it means keeping it up to date is automatic and handled by system-standard tools, unlike the vast majority of Mac software, which in the best case provides their own update mechanism (which is usually not quite as offensive as all the little update icons that end up on a Windows machine by the time it is fully functional, but it's still really irritating).

Mac OS X instead relies on a convention of bundling all necessary files together into an app bundle that's self-contained (and represented as such) and thus can be treated by the user as a cohesive, unitary Thing.

Yeah, I know. I've worked on a couple of very large "Things" of this sort in the past, when making packages of software I worked on for Mac OS X. I didn't call them "Things", though. I called them "Big Balls of Crap".

It's a horrible kludge that barely works, no matter how much you want to call it "empowering". Is it empowering to have the system make it trivial for a user to overwrite new versions with older, possibly insecure, versions without warning? Is it empowering to have no standard location for files of various types? Is it empowering to make it impossible to replicate an installation stack automatically across many systems using standard tools? Is it empowering to make software that cannot be managed from the command line? Is it empowering to have no standard mechanisms for knowing what is installed and what version? Is it empowering to possibly be running old and insecure versions of dozens of applications without even knowing it? Is it empowering to only have the features that the application bundler thought to include...things like checking to be sure there's enough disk space, checking to be sure the destination paths exist and are writable, keeping a record of what files ended up where, etc.? I've installed Mac OS X software that failed to do all of those things at one point or another, and ended up with a broken installation, usually without warning.

Look, if you like the pretty picture that applications display when you open up a dmg file or a CD, and you like the big shiny icons, and such, that's great. But don't hold up a gigantic gaping misfeature in Mac OS X as a positive thing. It's really not.

The average computer user is not better off with a dramatically worse implementation of package management, just because it usually won't end in tears.