Create the jail
Run these commands inside the jail.

1. pkg install python
2. pkg install ffmpeg
3. pkg install handbrake
4. Filebot (optional): Extracted the portable package into a folder in the jail -- Screenshot
5. pkg install libass
6. portsnap fetch
7. cd /usr/ports/audio/lame
8. make install clean (just keep hitting enter till it's finished)

Make sure the jail can access your encoding / media storage

I used this python script and commented out import ntfsutils.junction (Line 63)

and then changed these lines:

FFMPEG = '/usr/local/bin/ffmpeg' #'/usr/bin/FFMPEG'
HANDBRAKE = "/usr/local/bin/HandBrakeCLI" #'/usr/bin/HandBrakeCLI"
FILEBOT = '/filebot/filebot.sh'

Run the Python Script in the jail:

root@encoder_jail: nohup python conv2mp4.py &

Thanks to @KameeCoding & https://www.reddit.com/user/infinull for helping me get it working.