Just meditating, but to me it makes perfect sense to me that the directory search path comes in this order, especially when it comes to core. I think it follows a philosophy of 'adding on' modules, not 'enhancing existing' modules with over-rides. I think the distribution directories should contain nothing but core, tested and proven to work in harmony with the rest of the OS and attempting to upgrade them should not be taken lightly with a simple user search path over-ride. From an application point of view we're quite comfortable with over-riding just about anything in Perl, but from an OS point of view, I don't think you want that to happen (easily anyway).
What shocks me is that the core modules that Apple broke where 'upgraded' by users because the the Apple versions were old and out of date. The finger pointing at search path order seems to have overshadowed the fact that Apple has neglected to keep it's Perl core up to date.