You make a good point about not using the user's module updates for the system tools. However, the system tools should normally be run as a superuser account, which shouldn't normally be used for day-to-day production programming.
Beyond that, even system-wide system-specific module upgrades shouldn't change anything for OS distro utilities that use the modules. If they're packaging perl, the Perl modules, and packaging the apps that depend upon those modules, then the packagers of those dependent apps should have no problem knowing and using the exact paths to the original versions. There's even an optional vendor_perl directory one can configure during the perl build that's just like the site_perl directory. Mandriva uses it, so why not Apple?
I can understand the hesitation for a company that sells products based on "it just works" to bundle the latest and greatest software in their distribution all the time. I'm sure they only use things they're had time to test as units and in integration. While being on the cutting edge is great for some, when you're selling boxes to lots of people and want few support issues, you usually do stay back a few releases for stability and testing reasons.
