The versions in ports deal with dependecies on non-Perl libraries. For example, p5-XML-LibXML depends on libxml2, but the CPAN module XML::LibXML has no way of specifying a dependency on the libxml shared library.
If you use a perl binary installed through ports/packages, any CPAN module you install automatically generates a package using BSDPAN. Packages installed with BSDPAN list all files installed, but do not deal with any dependencies.
Sometimes, ports may contain FreeBSD-specific patches, but port maintainers should always submit patches back to CPAN authors.
See perldoc BSDPAN on your machine to find out if you use BSDPAN. pkg_info -I 'bsdpan-*' shows which packages BSDPAN has installed.
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