Filter with additional form element
You probably need to override the valueValidate method to tell it about the new structure:
protected function valueValidate($form, FormStateInterface $form_state) {
  $uids = [];
  if ($values = $form_state-&gt;getValue(['options', 'value', 'existing_element'])) {
    foreach ($values as $value) {
      $uids[] = $value['target_id'];
    }
    sort($uids);
  }

  $checkbox_value = $form_state-&gt;getValue(['options', 'value', 'new_element']);
  // Do something with $checkbox_value here as you're going to lose it

  $form_state-&gt;setValue(['options', 'value'], $uids);
}