Directories and directory permissions

[TheDreadPirate]

Would you move the config directories as well?

Depends.  Since the container runs as your user, its fine to leave it in your home directory.  Personally, I keep all my container's data in a root level folder (/docker) since I run a bunch of containers, many that run as users other than me.  It also simplifies backups to keep the containers all together.  If you only intend to run Jellyfin, just leave your /config directory where it is.

Also when talking about best practices (knowing that this forum is not a place to discuss Linux things), would you recommend that I also move my personal files (e.g. family pictures and such) from the home directory of SMB shares? I know this is very far from Jellyfin and basically a data management question but since you seem to have at least any kind of opinion on this, I thought I could ask.

Depends on whether your SMB share requires credentials or allows guest users.  If you require credentials and prohibit guest users, it is probably fine.