[robhlt]

The "Jellyfin for Kodi" plugin (not Jellycon!) supports a "native path" streaming mode that just directly passes the raw video file to Kodi, avoiding Jellyfin's transcoding entirely. I've never used it with BDMV's, but it does work with other formats Jellyfin can't transcode properly like Dolby Vision.

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.

[Borealid]

The reason I'd use Jellyfin is to stream things to a non-Kodi client (a web browser). If I have a Kodi client, I would just read the files as-is.

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.