When I create rules based on a taxonomy, the emails only go out to the default (admin). I believe you are finding these rules in your code, however you are not assigning their values to the $post_type_moderators variable. You should add at line 415 of wordpress-collaboration-emails.php (in 1.6.2):
$post_type_moderators = $post_type_rule->moderators;
Hope this helps!