I ran with a combination of Roy, tye, and Zaxo. s///e to get multiple lvalues into a string (one lvalue per line in the string), then Roy's idea to walk pos() in that line followed up with some modifications to substr() lvalues.

s(^(.+?\Q$RESET | \E)(.+)){
    my $header = $1;
    my $comment = $2;

    $comment =~
        s((?: <code> (.*?) </ code>
            | \[     (.*?) \]
            | (<!--  .*?   -->)
            )){
            ( ( defined( $1 ) && ( GREEN  . $1 ) ) ||
              ( defined( $2 ) && ( RED    . $2 ) ) ||
              ( defined( $3 ) && ( YELLOW . $3 ) ) )
            . RESET
        }gex;

    "$header$comment";
}meg;
[download]