Allow administrator to chose upload folder for files

Note that the custom properties doesn't seem to support tokens so one might need to extend the WebformManagedFileBase and in that new class override the getUploadLocation.

As I needed token support, I did it so that I created new WeformElement extending the WebformManagedFileBase that introduced new field where the upload location can be entered. Then in getUploadLocation get the new field value from $element, run $this->replaceTokens($element) and then call the parent getUploadLocation.

namespace Drupal\my_module\Plugin\WebformElement;

use Drupal\Core\Form\FormStateInterface;
use Drupal\webform\Plugin\WebformElement\WebformManagedFileBase;
use Drupal\webform\WebformInterface;

/**
 * Custom version of the webform document file.
 *
 * @WebformElement(
 *   id = "custom_webform_managed_file",
 *   label = @Translation("Custom managed file"),
 *   description = @Translation("Custom version of the webform managed file."),
 *   category = @Translation("File upload elements"),
 *   states_wrapper = TRUE,
 *   dependencies = {
 *     "file",
 *   }
 * )
 */
class CustomManagedFile extends WebformManagedFileBase {

  /**
   * {@inheritdoc}
   */
  protected function defineDefaultProperties() {
    return parent::defineDefaultProperties() + [
      'file_directory' => '',
    ];
  }

  /**
   * {@inheritdoc}
   */
  public function form(array $form, FormStateInterface $form_state) {
    $form = parent::form($form, $form_state);

    $form['file']['file_directory'] = [
      '#type' => 'textfield',
      '#title' => $this->t('File directory'),
      '#description' => $this->t('Optional subdirectory within the upload destination where files will be stored. Do not include preceding or trailing slashes.'),
    ];

    return $form;
  }

  /**
   * {@inheritdoc}
   */
  protected function getUploadLocation(array $element, WebformInterface $webform) {
    if (empty($element['#file_directory'])) {
      return parent::getUploadLocation($element, $webform);
    }
    $uriScheme = $this->getUriScheme($element);
    // Replace tokens.
    $this->replaceTokens($element);
    // Alter the element so we can call parent.
    $element['#upload_location'] = $uriScheme . '://' . $element['#file_directory'];

    return parent::getUploadLocation($element, $webform);
  }

}

Remember to create an element matching the ID of the webform element

<?php

namespace Drupal\ssp_site\Element;

use Drupal\webform\Element\WebformManagedFileBase;

/**
 * Provides a webform element for an 'custom_webform_managed_file' element.
 *
 * @FormElement("custom_webform_managed_file")
 */
class CustomManagedFile extends WebformManagedFileBase {

}