How to set an encrypted file field's value programmatically

Question

I'm trying to set an encrypted file field's value programmatically. I'm using Encrypted Files module. I have successfully configured a file field, and it works for the contents created using the node add form.

In a custom code, I'm getting a file using the HttpClient and want to attach to a media. I could get the file, encyrpt and save it. However, if I want to open the file, it is broken.

What I'm doing is like the following:

  $client = Drupal::httpClient();

  // Get data from remote page and encrypt using the encryption profile
  $data = (string) $client->get('https://example.com/download.php?file=123')
    ->getBody();
  $encryptionProfile = Drupal::entityTypeManager()
    ->getStorage('encryption_profile')
    ->load('my_encryption_profile');
  $encryptedData = Drupal::service('encryption')
    ->encrypt($data, $encryptionProfile);

  // Create media entity and prepare destination directory
  $media = Drupal::entityTypeManager()->getStorage('media')
    ->create(['bundle' => 'my_media_type']);
  $destination = 'encrypt://my_encryption_profile/path/to/files'
  Drupal::service('file_system')
    ->prepareDirectory($destination, FileSystemInterface::CREATE_DIRECTORY);

  // Save data as file and attach to the media
  $filename = 'download.pdf';
  $file = file_save_data($encryptedData, $destination . '/' . $filename);
  $media->set('encrypted_file', ['target_id' => $file->id()]);
  $media->save();