I know this issue is old, but I found it useful to edit the plugin http://ww.wp.xz.cn/extend/plugins/manage-tags-capability/
I just deleted the if inside of the function __construct(). In that way all the users have checkboxes instead of the input box.
Also instead of editing the functions.php I just added my custom post type in the array in the first line of that same function.
I hope that helps to someone else.
