Issue #1712352 by sun, effulgentsia: configuration system does not support themes.

core/modules/system/system.install

@@ -507,13 +507,15 @@ function system_requirements($phase) {
  * Implements hook_install().
  */
 function system_install() {
-  // Enable the default theme.
+  // Enable the default theme. Can't use theme_enable() this early in
+  // installation.
   variable_set('theme_default', 'stark');
   db_update('system')
     ->fields(array('status' => 1))
     ->condition('type', 'theme')
     ->condition('name', 'stark')
     ->execute();
+  config_install_default_config('theme', 'stark');
 
   // Populate the cron key variable.
   $cron_key = drupal_hash_base64(drupal_random_bytes(55));

core/profiles/standard/standard.install

@@ -419,11 +419,7 @@ function standard_install() {
   menu_router_rebuild();
 
   // Enable the admin theme.
-  db_update('system')
-    ->fields(array('status' => 1))
-    ->condition('type', 'theme')
-    ->condition('name', 'seven')
-    ->execute();
+  theme_enable(array('seven'));
   variable_set('admin_theme', 'seven');
   variable_set('node_admin_theme', '1');
 }