Permanent Deleting of files still doesn't work for me (make_unused_managed_files_temporary = true)
I just made a solution that works for me even the Drupal or config doesn't works properly. In my plugin I hooked up the hook_cron() for logging these unused files to proceed them next.

SQL SELECT; query to fetch all file_managed fid's. You can select only status=1, as permanent files, but I got all,
PHP loop all id's and making a Drupal\file\FileInterface entity reference $file = File::load($item-&gt;fid) to check all the file references $references = file_get_file_references($file). When the $references is empty() this file is unused. Save all that fid id's into array $fids,
SQL UPDATE; build update query to null these rows: UPDATE file_managed SET status=0 WHERE fid IN($fids) and UPDATE file_usage SET count=0 WHERE fid IN ($fids).

Finaly after next cron run the default function file_cron() {... will properly delete these files.