Oh, wait, now I understand. The first member of the array is the header! I can see now what you mean by "merge", I imagined something different, which did not happen. I apologize for offending your code. Here is how I would do it. How sexy it is depends on the beholder's perspective:

#!/usr/bin/perl
use warnings;
use strict;

use Data::Dumper;

my $arr = [[qw/name pos   loc age/],
           [qw/ike  boss  12  44/],
           [qw/mat  slave 22  21/],
           [qw/jill sec   15  32/],];

my $add = [[qw/car dog  age/],
           [qw/a1  grr  3/],
           [qw/s2  miew 7/],];

my $i = 0;
my %headers;
for (@{ $arr->[0] }, @{ $add->[0] }) {
    $headers{$_} = $i unless exists $headers{$_};
    $i++;
}

my $result = [ [ sort { $headers{$a} <=> $headers{$b} } keys %headers 
+] ];

my $new_columns = keys(%headers) - @{ $arr->[0] };
for (1 .. $#{$arr}) {
    push @$result, [ @{ $arr->[$_] }, (q()) x $new_columns ];
}

my @rearranged = map $headers{$_}, @{ $add->[0] };
for my $row (1 .. $#{$add}) {
    my @new = (q()) x keys %headers;
    my $i = 0;
    $new[$_] = $add->[$row][$i++] for @rearranged;
    push $result, [@new];
}
print Dumper $result;
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