Secondly, a BDMV can't be turned into a single correct linear representation - for example, the Star Trek TOS discs have the ability to toggle back and forth between original and CG-remastered graphics seamlessly. As another example, I have stereoscopic 3D blu-rays; should the transcode be the left eye view, or side-by-side 3D with an ultrawide file?
Finally, transcoding necessarily sacrifices quality. Remuxing wouldn't, but Jellyfin usually refuses to stream remuxed containers and insists on transcoding to attach subtitles (their javascript web player and even app don't seem to handle the subs correctly?).
To sum up, turning a disc folder into a single file requires losing content.
The stuff that Jellyfin would provide - being able to watch from a device using just a web browser and no client install - is nice-to-have, not need-to-have.
Also, if you do ever want to remux those discs, mkv does support both those features now (player support is lacking though). You'll want to look for "3D MVC" support, and including 2 video tracks in one mkv is no problem.
I don't believe that mkv supports bd-j menus. Happy to be proven wrong on that if you have some further reading I could do.