Final Solution based on accepted solution from @4k4 (see answer).

<?php
use Drupal\Core\Database\Database;
use Drupal\Component\Serialization\Yaml;
use Drupal\Component\Utility\NestedArray;
use Drupal\field\Entity\FieldStorageConfig;
use Drupal\field\Entity\FieldConfig;
use Drupal\Core\Utility\UpdateException;

/**
 *  Add required fields to user entities.
 */
function {module}_update_9001(){
  $modulePath = \Drupal::service('extension.list.module')
        ->getPath('{module}');
  $configPathStorageObjects = \Drupal::service('file_system')
    ->scanDirectory($modulePath.'/config/optional','~field\.storage\.user\..*~');
  \Drupal::logger('staffdb')->notice('storage objects: <pre>'.print_r($configPathStorageObjects,true).'</pre>');

  //add missing field storage
  foreach ($configPathStorageObjects as $configPath){
    $config = FieldStorageConfig::loadByName('user',str_replace('field.storage.user.','',$configPath->name));
    if(is_null($config)){
      $configSettings = Yaml::decode(
          file_get_contents(
            "$modulePath/config/optional/{$configPath->filename}"
            )
          );
      $fieldStorage = FieldStorageConfig::create($configSettings);
      $fieldStorage->save();
    }
  }

  //add missing fields to users
  $configPathFieldObjects = \Drupal::service('file_system')
    ->scanDirectory($modulePath.'/config/optional','~field\.field\.user\.user\..*~');
  foreach ($configPathFieldObjects as $configPath){
    $config = FieldConfig::loadByName('user', 'user', str_replace('field.field.user.user.','',$configPath->name));
    if(is_null($config)){
      $configSettings = Yaml::decode(
          file_get_contents(
            "$modulePath/config/optional/{$configPath->filename}"
            )
          );
      $field = FieldConfig::create($configSettings);
      $field->save();
    }
  }
}