One issue in particular that took a minute to figure out with docker, if you need the containers to talk to eachother, you have to be aware that certain types of docker network connections will not automatically see the other containers, even if both containers are connected to your home network.

Yup, this is exactly the issue I haven't been able to figure out. For some reason, the files I download in Sonarr are associated with a user group that Plex isn't a part of, so Plex can't see the files (and I've tried adding Plex to that group and it still doesn't work, argh). I know you can specify a UID and other specifics when you initialize a container, but inside the container itself that doesn't seem to apply, it sets its own user parameters. I'm about ready to throw in the towel and just run the software on my machine itself with a VPN, because then at least everything will be able to talk to each other.