how should I hide the menu and url setting in from alter?
As explained in hook_form_alter


  The call order is as follows: all existing form alter functions are
  called for module A, then all for module B, etc., followed by all for
  any base theme(s), and finally for the theme itself. The module order
  is determined by system weight, then by module name.
  
  Within each module, form alter hooks are called in the following
  order: first, hook_form_alter(); second,
  hook_form_BASE_FORM_ID_alter(); third, hook_form_FORM_ID_alter(). So,
  for each module, the more general hooks are called first followed by
  the more specific.


So, your module hook_form_alter is called before path module or menu module which adds those elements. That's the reason you can able to see those elements when you print form in your custom module.

Try using same form alter hook in your theme template.php it should work. It worked for me ! I can able to see path settings and menu setting. See for Seven Administration theme below.

function seven_form_alter(&amp;$form, &amp;$from_state, $form_id) {
  drupal_set_message("&lt;pre&gt;" . print_r($form, 1) . "&lt;/pre&gt;");
}


Else, you need to alter your module weights !!