Are you chasing a specific quality problem? If you can demonstrate better settings, you might have more luck encouraging Plex to adjust the default settings.
If you search the forum for TranscoderH264OptionsOverride you’ll find some ancient comments. There are some additional reasons the behavior may be different, too.
There have been a few interesting hacks where people swap out the Plex Transcoder binary with a script, and use that script to match-and-edit the arguments. A couple links here -
Script to regenerate video previews multi threaded? - #9 by Volts
