The Downloaded Episodes Scan feature only scans the contents of the man directory which is specified; subdirectories are skipped.
My Transmission automatically downloads to this folder, but puts all the downloads in subdirectories (< downloaddir>/<series.s01.e01>/filename.mkv). These files are not imported, and I have to move them manually to < downloaddir>.
Drone Factory (Downloaded Episodes Scan) either needs the file to be in the root for the folder Sonarr is told to scan or in a folder that Sonarr can identify as being for a specific series (either the release name or a folder with just the series name).
With Transmission (and all torrent clients) you should be using Complete Download Handling to import so seeding torrents are hardlinked or copied instead of moved though.
Complete Download Handling is enabled (and works fine voor SABnzbd), but doesn’t do anything with Transmission, so I was looking for alternatives to make this work automatically.