...where the key is a string, but the value is an array

You could try something like this: 

#!/usr/bin/perl

use strict;
use warnings;
use Getopt::Long;

my $myopts = {};
my $curr_opt = '';
my $curr_key = '';

sub first_opt {
    $curr_opt = shift;
    $curr_key = shift;
    add_opt(shift);
}

sub add_opt {
    my $val = shift;
    $val =~ s/,$//;
    push @{$myopts->{$curr_opt}{$curr_key}}, $val;
}

# some commandline input
{   no warnings "qw";
    @ARGV = qw(
      -cmdline_option1 REG1=value1, value2, value3, value4
      -cmdline_option1 REG2=Value1, Value2, Value3, Value4
      -cmdline_option2 REG1=val1, val2, val3, val4
      -cmdline_option2 REG2=Val1, Val2, Val3, Val4
    );
}

GetOptions (
            'cmdline_option1=s%' => \&first_opt,
            'cmdline_option2=s%' => \&first_opt,
            '<>'                 => \&add_opt,
           );

use Data::Dumper;
print Dumper $myopts;

__END__
$VAR1 = {
          'cmdline_option2' => {
                                 'REG1' => [
                                             'val1',
                                             'val2',
                                             'val3',
                                             'val4'
                                           ],
                                 'REG2' => [
                                             'Val1',
                                             'Val2',
                                             'Val3',
                                             'Val4'
                                           ]
                               },
          'cmdline_option1' => {
                                 'REG1' => [
                                             'value1',
                                             'value2',
                                             'value3',
                                             'value4'
                                           ],
                                 'REG2' => [
                                             'Value1',
                                             'Value2',
                                             'Value3',
                                             'Value4'
                                           ]
                               }
        };

[download]

In reply to Re: Processing Complicated Command Line Options using Getopt by almut
in thread Processing Complicated Command Line Options using Getopt by ganeshts

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