Perl is being removed from the core build process for FreeBSD as of FreeBSD 5.0. So what.
A lot has been made of the interaction between Perl 5.005_03 (part of /usr/src), FreeBSD, and keeping a more modern/customized build of Perl on a FreeBSD system. Yet another tempest in a teapot. (Tempest in a teaspoon, actually).
Dear reader, be advised that the interaction between Perl5.005_03, FreeBSD, and your very own custom Perl is a complete non-issue.