Why would the user need to manage the docker containers? I see the panel managing the containers as far as creating, mapping, updating. The average user doesnt even know they are docker containers.
The linuxserver.io guys update the apps regularly on them or they are automatically updated on restart(the plex one does this). The QB panel could check for an update and prompt to ask the user if they want to update or prompt to restart the app. Plex one has a variable for version..ala PlexPass or normal, etc.
The config files for the apps would be mapped to the /home/user/config/my_app directory where you could customize it as needed.
I rarely, if at all, have to connect into the actual container to do any manual work but obviously advanced users can do that if they wanted to.