I use Docker for my setup and mistakenly had my qBittorrent download folder and my *arr media folders mounted as /downloads and /movies as opposed to /arr/downloads and /arr/movies

The *arr programs running inside their containers don’t know that the two folders are actually on the same drive because it sees them as two separate mount points. Once I changed my *arr containers to mount my directories correctly, the hard linking worked as expected instead of copying files over. I then ran fclones and recovered over 700 GB of storage from deduplication.

I had a few metadata issues with Jellyfin until I changed the primary metadata source to be the same as what Radarr/Sonarr use so they all the file names match up and I’ve had no issues since.

I also don’t have a notable issues with subtitles in Jellyfin, but maybe your requirements have more friction. Have you tried the (iirc included by default) Jellyfin plugin to automatically download subtitles for your stuff? Or the *arr program that handles subtitles (I forget its name)?