Let's have a look at your data:

#! /usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

# this remains a plain array!
#   '=>' is a 'fat comma', so we have a simple list
#   with '=>' you don't need to quote the string to its left
my $in = [ one => 1, two => 2, two => '2.003' ];
print Dumper( $in );

__END__
$VAR1 = [
          'one',
          1,
          'two',
          2,
          'two',
          '2.003'
        ];
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To transform the array into a hash (of arrays), the following should do the job:

my %hash;
while ( my ( $key, $val ) = splice( @$in, 0, 2 ) ) {
  push @{ $hash{$key} }, $val;
}
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Update:

• Inserted short explanation about "fat comma" into code