only in patch2:
unchanged:
--- a/core/modules/system/src/Form/ModulesListForm.php
+++ b/core/modules/system/src/Form/ModulesListForm.php
@@ -199,7 +199,6 @@ public function buildForm(array $form, FormStateInterface $form_state) {
     uasort($modules, 'system_sort_modules_by_info_name');
 
     // Iterate over each of the modules.
-    $form['modules']['#tree'] = TRUE;
     foreach ($modules as $filename => $module) {
       if (empty($module->info['hidden'])) {
         $package = $module->info['package'];
@@ -234,6 +233,7 @@ public function buildForm(array $form, FormStateInterface $form_state) {
     // Lastly, sort all packages by title.
     uasort($form['modules'], array('\Drupal\Component\Utility\SortArray', 'sortByTitleProperty'));
 
+    $form['modules']['#tree'] = TRUE;
     $form['#attached']['library'][] = 'system/drupal.system.modules';
     $form['actions'] = array('#type' => 'actions');
     $form['actions']['submit'] = array(