I would do it in a two-way approach, first splitting up the template into literal parts and TT code, and then stripping out the TT comments, maybe:

use strict;
use warnings;
use Data::Dumper;
$Data::Dumper::Useqq = 1;

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
%]
TT

my @parts = ($tt =~ /\G(
                       (?:[^\\\[]+)    # not a template, not a backsla
+sh
                      |(?:[\\].)       # an escaped whatever
                      |(?:[\[][^%])    # not a template, [ followed by
+ whatever
                      |(?:\[%.*?%\])   # within a TT template
                     )
                    /msgx);

@parts = 
         map { s!\s+#.*$!!gm; $_ }    # comments up to EOL
         map { /^\[%#/ ? "" : $_ }    # TT comments
           @parts;

warn Dumper \@parts;
[download]

This will not deal well with templates containing code containing a literal %]. So, don't do that.