Is package management really at issue here? For Apple supplied software, I think it really boils down to the same thing as other distros/OSes: timeliness of security updates. If Apple isn't able to spin out incremental security updates as quickly as other distributions, I'd say that process issue is the real problem.

Honestly, there's also something to be said for two-tier package management, ala OS X with Homebrew. Self-contained third party apps get a more managable space of base system profiles to target, and the installation UX can be as simple as drag/drop/app works. Us "special needs" users can then layer on and manage more esoteric and/or cutting-edge tools as needed with a full package manager. Heck, I was really glad to see Linuxbrew finally come to fruition for this very same reason. Have your cake and roll a newer-than-distro version of your tools too!

Homebrew (http://brew.sh) is pretty darned solid.

It should do, but if an application wants to use /usr/bin/git for some reason they can still just do that!