Yeah... same story. I have couple of hundreds of .ts files which I need to convert to .mkv, strongly preferably -- without transcoding. Gave up on mkvmerge, found that ffmpeg does it nicely, harried for ffmpeg docker... oops. Not in Community Applications. Not in Nerd Pack. Small nice docker "convert2mkv" requires all files in one place and each and every way I tried to make it load/output from other directories failed. Even provided symbolic links in the directory -- nope. Tried half dozen ffmpeg dockers from Docker Hup -- neither will start, I gave up on them too.
Will look for no-transcoding mode in HandBrake, and if no, my only way would be to install ffmpeg on my Windows laptop and do conversions over the network...