Regarding transcoding (Scouting document page 12): can transcoding be initiated manually or does it have to be initiated by an upload process?

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
are possible.

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.