But then if you have /home in the config file, you should not print /home/foo? (I did not understand that too well) If you are going to have only high level directories (and by that I mean subdirectories in /), and the directories you have to decide wether or not to print are subdirectories of these high level ones, then I guess you could strip everything after the second '/' and then make a direct comparaison...

sub print_report {
    foreach (keys %$dirs) {
        print BENCHMARK $_;
        m#^/[^/]+/#;
        next if defined $config_dirs->{$&};
        print "$_\n";
    }
}
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(I hope I understood the problem correctly)