The torrent client can get confused about the authenticity of the files if you make any changes to the files that were downloaded. It can also have trouble finding all the files required for seeding, so moving the needed files to media is a no.

Once the torrent client finishes downloading the files, instead of copying the needed files among them to media’s respective folder, we simply make a hardlink to it to save space and to ensure the authenticity of the files in torrents folder such that the torrent client has no trouble seeding the files.

The seeded folder which contains the needed files can also contain media that can potentially confuse Jellyfin such that it shows it; furthermore, less useless files also increases the scanning time taken by Jellyfin. So instead of directly linking the respective folders in torrents we have a separate and more clean directory for Jellyfin media.

TL;DR: to save space and to ensure your torrent client can keep seeding the files.