If the torrents are still seeding when the import in arrs happens, it would copy the file(s) to your media folder so you’d have two copies now. If the torrent is done seeding and, I think if you have completed download handling enabled, it’ll do a move instead so you’d end up with only one copy.

Ideally though you want a hardlink compatible setup but from what you said you do not.

Jellyfin just monitors your media folder which is managed by the arrs.