anytom4v
This is a shell script I developed a while back, first to automate HandBrake from the command line, then to automate ffmpeg in a similar manner. As it stands now, it accepts input in whatever formats ffmpeg accepts and transcodes to H.264 video with aggressive compression but still decent (IMHO) quality and HE-AAC audio. Simple options to do things like detelecine, PAL-to-NTSC conversion, and inclusion of subtitles (they're normally excluded) are available; run with -h to see what you can do.
Now the script is containerized, and can be invoked with something like:
docker run -it --rm -v /mnt/files:/mnt/files salfter/anytom4v -o /mnt/files/video.m4v /mnt/files/src_video.mkv
Development is over at https://gitlab.com/salfter/anytom4v-docker.
Update (9 Jun 22): Switched the base container from Debian to Gentoo, as the script was developed on Gentoo and uses options that apparently aren't in Debian builds of ffmpeg.