The easiest tool is MakeMKV. But you’ll often encounter opportunities for efficiency (eg stereo DTSHD to FLAC) as well as requirements to convert* for hardware compatibility. That’s where ffmpeg and MKVToolNix are good secondary tools for customizing the remux contents.
*Not transcoding. Rather, lossless formet 1 -> lossless format 2.
A crass nickname for the CIA Prize for Journalism if I ever saw one.