I usually check the length of each episode with the disc open in VLC and find the title with a matching length in MakeMKV, so I can set the names before extracting. Jellyfin supports naming episode files ‘S01E01 Episode Name’ which makes it easy to track what the file really is in case the db ordering turns out to be different. For nonserialized shows where order mismatches are likely I’ll check with TVDB as I’m going through the episodes on the disc.