Yes, this can be initiated manually too. And, like you already wrote, it can be initiated by an upload process even with the FTP bulk upload by putting the right commands in the VUF file. Even multiple transcodings
We recently even have a command line tool for administrators to start any transcode or re-analyze possible. It is based on Drush, a Drupal add-on for command line actions. Very useful for batch operations. FTP is also very powerful for this.