Sometimes correct operation of a Perl application depends on a specific combination of the versions of installed modules. By bundling a custom installation with your app, you can increase the probability your app will run correctly on a system other than your development machine.
Of course, it would be better to test your app on several very different systems to weed out such dependencies. And if you aspire to have your app available as a package in your favorite Linux/BSD/whatever distribution, you need to make sure it works with the default Perl installation for that distro (which is often very very old and often lacks many very useful modules).
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