Sorry for the late reply;
If i leave the automated download handling on, then sonarr will move the completed video file to the TV shows folder. (At least with the transmission download client)
So then it would bypass the handbrake watch folder.
And it is indeed not an issue for plex, but it could be annoying to search for a movie and not find it in plex only to find out that it is still in the watch folder with a 1000 other movies.
Oh and I just thought of this, but if this container would move the video file inside the container (tmpfs) before encoding it, then we would avoid having 2 hosts encoding the same file .