It took me some time to read up on Docker and how to use it properly. Per your request I have made a Docker container of my current Prod. ENV and provided you a link in your private inbox as requested. I will review the ffmpeg configuration information on my other system with ffmpeg install, which I will note returned a different error then the Kaltura CE version of the ffmpeg installation. My guess is if I find the differences in the the configurations settings and add the missing configurations to each system the encoding command will work without the errors.
Specifically, the Timestamps error does not show on my non-Kaltura system but the error related to opening the stream on that system does not appear on the Kaltura CE system. I will work on this from my end and update you with my progress as you attempt recreate the issues on your end to find a solution.