I know nothing about bioinformatics but have you tried using the object returned by ->align in the iterator loop ?

#!perl
my $factory = Bio::Tools::Run::Alignment::Clustalw
              ->new(-matrix => 'BLOSUM');
.
.
.
my $alnio = $factory->align($seq_array_ref);
while( my $aln = $alnio->next_aln ) {
  .
  .
}
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