If you look at the processes on your device while an optimization job is active, you can see how the Plex Transcoder was instantiated. All of the arguments are visible. Or you can see the history in Plex Media Server.log. Some of the arguments are Plex-specific like --progressurl but you can decode the “familiar” ffmpeg stuff easily enough.
Additional steps are required to actually call the Plex Transcoder yourself - you need to set some environment variables. Plex is doing some clever stuff to separate the open-source and non-open-source bits of code. Like @trumpy81 I would strongly discourage you from using it as your day-to-day encoder.
I mention a few of the other environment variables here:
https://forums.plex.tv/t/transcoder-background-tasks-being-throttled/
What’s interesting about the “Optimize …” presets is that they’ve got VBV enabled with bitrate targets focused on remote streaming. I don’t think they’re ideal “Archival” settings, but if you’re keeping your DVDs you can always do another “good” encoding from source.
