As @gorgarp123 posted his project here, I realized that I had never thought to do the same. I built a similar project a while ago called Plexus which has native RClone support and various other configurable options.
The idea is that you build a list of your media via plexus list -a "aac" -v "x264" -d "/path/to/media" and then encode that list via plexus encode -a "aac" -v "x264" or with the -r RCloneRemote: flag for direct RClone support. A list is used (instead of in-place encoding) so that you can stop and resume encoding at any point.
You can specify different codecs via CLI flags or by using the config file:
audio_codec="aac"
convert_dir="$HOME/.plexus/encode/convert"
converted_dir="$HOME/.plexus/encode/converted"
ffmpeg_binary="/usr/bin/ffmpeg"
ffmpeg_threads="2"
ffmpeg_preset="faster"
ffprobe_binary="/usr/bin/ffprobe"
force_overwrite="true"
list_file="$HOME/.plexus/list.txt"
media_container="mkv"
media_dir="/mnt/plexdrive"
mount_dir=""
rclone_binary="/usr/bin/rclone"
video_codec="h264"
video_library="libx264"
If you have any feature requests or other ideas, I would love to hear them 
You can find the repo here: GitHub - wolveix/plexus: A suite of tools to help manage your media collection.
