If you want to add a flag link on a form but instead of through formname.tpl.php you want to add through a function in template.php, you can still add using flag_create_link
For example to add this on comment form just above the text window You would need

$str= flag_create_link('flag_top_10', $form['nid']['#value']). "<br>Your comments ";
$form['comment_filter']['comment']['#title']  = t($str);