The perl ebuild script does not add the option -Dscriptdir=/usr/bin to Configure. The Configure script checks for /usr/share/scripts, /usr/share/bin, /usr/local/script, /usr/local/scripts and $prefixexp/script. So if one of these directories exist, Configure is using it as $scriptdir.
Actually, this was in the perl-module eclass, but there was a mix up in commits and was overwritten. This has been readded to the perl-module eclass, so any ebuild that inherits from it (as about 90% of ebuilds that use perl-modules do) will have the line added now. Let me know if this doesn't resolve your problem (if you don't see the line in the eclass/perl-module.eclass, emerge rsync - it was commited a few days ago, so there's no reason it shouldn't be on all of the mirrors by now).
Safe to close?
