Also, I found out that I can use '--' option. But it really feels to me as a workaround and I don't want to make the users use it.

I don't think it's a workaround, using -- to indicate "stop processing options here" is a really common thing - perl, git, GNU getopt, and many other tools do it, which is why Getopt::Long supports it.

I also don't think messing with @ARGV is a bad thing to do, especially since you'd just be looking for a fixed string.

use warnings;
use strict;
use List::Util qw/first/;

@ARGV = qw/create --folder empty --size 50
    --additional hey how ---are --you 555/;

my $i = first { $ARGV[$_] eq '--additional' } 0..$#ARGV;
my (undef,@add) = defined $i ? splice @ARGV, $i, $#ARGV-$i+1 : ();

use Data::Dump;
dd \@ARGV, \@add;

__END__

(
  ["create", "--folder", "empty", "--size", 50],
  ["hey", "how", "---are", "--you", 555],
)
[download]

Admittedly not the most beautiful code, but it works. If you want more elegance, I'd suggest either -- or hippo's suggestion...