qBittorrent-nox is as separate as you can get. It can be run on the server without GUI. It also provides WebUI, that can be modified if you wish, but you don’t have to use it. Moreover, most (if not all) settings can be edited through the text file and torrents added using CLI.
qBittorrent, when Web-UI is enabled (doesn’t matter if it’s nox or not), provides and API too. IF you have a client you can connect and manage everything using it. However, the only clients I know are for android.