Once you have both files as lists, you can use List::MoreUtils to test uniq-ness:

use Tie::File;
use List::MoreUtils qw(uniq);

tie my @file1, 'Tie::File', 'file1' or die;
tie my @file2, 'Tie::File', 'file2' or die;

print join "\n",uniq (@file1,@file2);
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