inc/inc2/index.php taken from login_inc/_inc2/_index.php. But, logic inside index.php/login_index.php will read custom-index.php, custom-inc.php and custom-inc2.php if exist.
So, it's simple to modified login page with customizing custom-index.php, custom-inc.php and custom-inc2.php without worry overwrite files if Kloxo-MR updated.