Installing debs with apt-get is easy-peasy and very reliable on any Debian system. No doubt.
But as for CPAN, ease depends in part on how one has set
up Debian. A C compiler and make isn't a given on Debian, for instance, and many CPAN builds will fail without one. Nor are various networking and system tools a given: ssh clients, sudo, and many others need to be explicitly downloaded if you do a minimal install. Debian has a huge variety of download options - from a minimal 40MB install to a 650MB CD image.
I haven't noticed problems with CPAN and apt-get/dpkg conflicting. However, that doesn't mean that there aren't conflicts with CPAN build scripts and Debian itself. Debian uses Perl as part of its own system core. It has a rather complicated policy to keep modules needed by the system separate from site installed modules and to prevent version conflicts between site and system versions. (see Debian Perl Policy). There is a reason why Debian spends so much time testing stuff for integration issues. Debian also sometimes has special versions of binaries that hard code Debian system locations. As a result, in general, I have found the .deb's retrieved by apt-get more reliable than CPAN - but they also tend to be several versions old and not everything on CPAN has a well tested .deb
There are also different tolerance levels for sysadmin problems and complications depending on whether *nix is running on a server managed by a professional system administrator or on the desktop machines of developers. Developers may know their programming language and design tools well but sometimes have only sketchy ideas of sysadmin issues, even when its their own development tools that are being installed by a deployment system. I rather doubt most monks fall in this category, but I've brought in team members for Java work who think I have horns when I tell them they *must* learn basic command line skills.
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