Exposed filter for taxonomy vocabulary behaves differently if exposed form element changed to checkboxes

Here is the exported view along with some additional information.

I notice that when the exposed filter form is unaltered the resulting SQL is:

SELECT node.nid AS nid,
   node.title AS node_title
 FROM node node 
 LEFT JOIN location_instance location_instance ON node.vid = location_instance.vid
 LEFT JOIN location location ON location_instance.lid = location.lid
 WHERE (node.status <> 0) AND (node.type in ('some_store'))

When the exposed filter form is altered the resulting SQL is:

SELECT node.nid AS nid,
   node.title AS node_title
 FROM node node 
 LEFT JOIN term_node term_node ON node.vid = term_node.vid
 LEFT JOIN term_data term_data ON term_node.tid = term_data.tid
 LEFT JOIN location_instance location_instance ON node.vid = location_instance.vid
 LEFT JOIN location location ON location_instance.lid = location.lid
 WHERE (node.status <> 0) AND (node.type in ('some_store')) AND (term_data.vid in ('0', '0', '0'))

This is how I am altering the form:

function custommod_form_alter(&$form, $form_state, $form_id) {
  switch ($form_id) {
    case 'views_exposed_form':
      // Make changes to exposed views filters
      if($form_state['view']->name == 'store_search') {
        // Change taxonomy vocab search from select to checkbox
        $form['vocabulary5']['#type'] = 'checkboxes';
      }
      break;
  }
}

Here is the exported view:

$view = new view;
$view->name = 'store_search';
$view->description = 'storesearch';
$view->tag = '';
$view->view_php = '';
$view->base_table = 'node';
$view->is_cacheable = FALSE;
$view->api_version = 2;
$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
$handler = $view->new_display('default', 'Defaults', 'default');
$handler->override_option('fields', array(
  'title' => array(
    'label' => 'Title',
    'alter' => array(
      'alter_text' => 0,
      'text' => '',
      'make_link' => 0,
      'path' => '',
      'link_class' => '',
      'alt' => '',
      'prefix' => '',
      'suffix' => '',
      'help' => '',
      'trim' => 0,
      'max_length' => '',
      'word_boundary' => 1,
      'ellipsis' => 1,
      'strip_tags' => 0,
      'html' => 0,
    ),
    'link_to_node' => 0,
    'exclude' => 0,
    'id' => 'title',
    'table' => 'node',
    'field' => 'title',
    'relationship' => 'none',
  ),
));
$handler->override_option('sorts', array(
  'distance' => array(
    'order' => 'ASC',
    'origin' => 'tied',
    'units' => 'km',
    'latitude' => '',
    'longitude' => '',
    'id' => 'distance',
    'table' => 'location',
    'field' => 'distance',
    'relationship' => 'none',
  ),
));
$handler->override_option('filters', array(
  'status' => array(
    'operator' => '=',
    'value' => '1',
    'group' => '0',
    'exposed' => FALSE,
    'expose' => array(
      'operator' => FALSE,
      'label' => '',
    ),
    'id' => 'status',
    'table' => 'node',
    'field' => 'status',
    'relationship' => 'none',
  ),
  'type' => array(
    'operator' => 'in',
    'value' => array(
      'some_store' => 'some_store',
    ),
    'group' => '0',
    'exposed' => FALSE,
    'expose' => array(
      'operator' => FALSE,
      'label' => '',
    ),
    'id' => 'type',
    'table' => 'node',
    'field' => 'type',
    'relationship' => 'none',
  ),
  'vid' => array(
    'operator' => 'in',
    'value' => array(),
    'group' => '0',
    'exposed' => TRUE,
    'expose' => array(
      'use_operator' => 0,
      'operator' => 'vid_op',
      'identifier' => 'vocabulary5',
      'label' => 'Taxonomy: Vocabulary',
      'optional' => 1,
      'single' => 0,
      'remember' => 0,
      'reduce' => 0,
    ),
    'id' => 'vid',
    'table' => 'term_data',
    'field' => 'vid',
    'relationship' => 'none',
  ),
));
$handler->override_option('access', array(
  'type' => 'none',
));
$handler->override_option('cache', array(
  'type' => 'none',
));
$handler = $view->new_display('page', 'Page', 'page_1');
$handler->override_option('path', 'storelocator');
$handler->override_option('menu', array(
  'type' => 'none',
  'title' => '',
  'description' => '',
  'weight' => 0,
  'name' => 'navigation',
));
$handler->override_option('tab_options', array(
  'type' => 'none',
  'title' => '',
  'description' => '',
  'weight' => 0,
));