With latest Plex bad move, I’ve uninstalled it and installed Jellyfin instead. I’ve asked Plex the same MK3D support but until then had to take mass-rename all my 3D collection to MKV to have it indexed.
Now that I have Jellyfin which support MK3D I did rename all the files to MK3D again. If this ever work in the future it would be nice to be able to stream without having to rename first.