Like kizer mentioned, make sure your watch folder has rw permissions. Also, make sure the environment variable is properly set (AUTOMATED_CONVERSION_KEEP_SOURCE=0). Finally, if you look at the container log, you should see a message telling that the source file is being removed. If you don't see it, then the environment variable is not set properly. Else, you may see an error if the watch folder is read-only.
Yes, I confirm this behavior. Will fix that...
Symlinks need to make sense from the point of view of the container, not the host. For example the following symlink, as seen inside the container, is good:
/watch/MyMovie.mkv -> /storage/media/Movies/MyMovies.mkv'
But not this one:
/watch/MyMovie.mkv -> /mnt/user/media/Movies/MyMovies.mkv'