Which “bug” ?
I created this one about two weeks ago: Bug report - Server restart resets Transcoding parameters
I then found a related bug report (fewer details) created two months ago: Plex Media Server configs after power failure
Neither of these has had any response from the Developers. No indication of someone doing any Triage on them to verify whether or not it’s real and to estimate dev-hours required to resolve. Not even someone asking for more details. 
There is no “man page” for the transcoder
You’re better off using FFMPEG directly
I had hoped that the integration of the output files would be better using the transcoder, but if I need to use FFMPEG, I guess that’s what I need to do.
It will take some time to put together a usable argument list for FFMPEG and to implement a batch/queue system to process the requests.
Of course, the two obvious alternatives are:
- Figure out a way to convince Plex that bug resolution really is important. Based on what I’ve seen here, the chances of that are somewhere between slim and none. I’ve seen “Bug Report” threads closed after three months because the developers were too interested in new features to bother with resolving bugs. This is the best way I know of to run a product into the ground.
- Migrate to a server app where the developers are actually concerned with fixing bugs.
