Format Expression refers to the custom naming scheme:
https://www.filebot.net/naming.html
--apply clean is a command-line option. The GUI will do
--apply prune by default
(cannot be disabled) and cannot do
--apply clean (cannot be enabled) so that you can't accidentally delete all your files.

However, you can create a *.cmd file and call the
cleaner script, and then call / double-click that on demand.

Personally, I would process all the files in the
/input folder as usual, and not worry about left-behind junk files at all, and then just delete the entire
/input folder and whatever is left inside at a later point in time, after all the video files have been moved to their final destination.