Create a hook_file_entity_presave_alter

We already have a way to designate custom file types via hook_file_type_info, but no way to let the assign an entity to a new bundle via this, as $file->type is automatically parsed via the mime type. It would be nice to expose a hook for this in file_entity_file_presave:

function file_entity_file_presave($file) {
  // Always ensure the filemime property is current.
  if (!empty($file->original) || empty($file->filemime)) {
    $file->filemime = file_get_mimetype($file->uri);
  }

  // Always update file type based on filemime.
  $file->type = file_get_type($file);
  
  //Allow other modules to alter the file object before presaving it. 
  drupal_alter('file_entity_presave', $file);

  field_attach_presave('file', $file);
}

That way you can now set the custom bundle and allow field_attach_presave to attach the fields from the proper bundle.

If there's interest, I can quickly submit a patch!