Ummm… I am not sure what you mean by having multiple “dockers” such as indexer, media server, downloader etc. Docker is a virtualization engine that runs applications in docker containers. I have one sonarr container, one radarr container, one sabnzbd container, one jacket container etc. running in docker all at once. The nice thing that docker solves is program dependencies as the containers are preconfigured with things like mono, databases, etc that are needed by the application. You do need to make sure that you are aware of volatile vs. non-volatile filesystems as filesystems that are within the container are destroyed if the container is updated so anything that should be permanent, (like media files systems or the sonarr configuration filesystem) should be on the host server and mounted by the docker container so even if you delete the container these file systems persist.
Another advantage that docker has is since it has its own network layer you can force your BitTorrent traffic through a VPN and let other things go out normally. In my case, I have my qBittorent container dependent on the nordvpn container and all traffic in and out of qBittorent is forced through nordvpn. Should the VPN go down or offline qBittorent is blocked. All that is easily configured in docker without going through complicated routing and firewall configuration.