Does this, untested, code help?

use strict;
use warnings;
use Getopt::Long;
my ( $cfg,$files ); 
my $output = 'Output.summary';
GetOptions ('cfg=s' => \$cfg, 'rtl=s' => \$files); 
open my $fh1, '<', $cfg    or die "Can't open $cfg: $!"; 
open my $fh2, '<', $files  or die "Can't open $files: $!"; 
open my $fh3, '>', $output or die "Can't open $output: $!";

# Read the config file first 
# less memory required assuming it is the smaller file
my @patterns;
while (<fh1>) {
    next unless /\S/; 
    chomp;
    push @patterns, $_;
}

my %results;
# Now look through the other file
while (my $data = <$fh2>) {
  next unless /\S/;
  chomp $data;
  for my $pattern (@patterns) {
    if (index $data, $element) { # don't need regex for exact match
      $results{$data} = "matches $element";
      last;
    }
    else {
      $results{$data} = "doesn't match";
    }
  }
}

while (my($key,$value) = each(%results)) {
  print $fh3 "$key => $value\n";
}
[download]

Cheers,
R.