I can't get that TT snippet to compile:

use strict;
use warnings;
use Template;

my $tt = <<'TT';
[% # this is a comment to the end of line
   foo = 'bar'
%]
<p>You might have an array in your TT</p>
[%
   #foo = bar[5];
%]
<p>bw, bliako</p>

[%# placing the '#' immediately inside the directive
    tag comments out the entire directive
%]

A nested tag:

[% # a comment
   abc = 1;
   [%# xyz %]
%]
TT

use Template;
my $parser = Template->new();
my $output = $parser->process(\$tt, { bar => [1,2,3,4,5]})
    or die $parser->error;
print $output;

__END__

file error - parse error - input text line 16-18: unexpected token (%#
+)
  [% # a comment
   abc = 1;
   [%# xyz %]
[download]

I still doubt that Template Toolkit supports nested comments, but again, if you have a regular expression for nested comments in C, I already showed you what you need to change in it to make it work for TT comments.