If you absolutely must do some config on the container, then have a container creation script that creates a new container with the right settings and use that.
This. They'll shut down for retooling, open up to churn out a small number of robots that do nothing, and claim success while firing most of the staff.
Hosting things in docker separates then from the OS and makes upgrading safer and easier.
Eventually, you'll want to update your OS. If the software is right on the OS, you might break it. If it's in docker and the machine breaks, run the container on another machine.
If you upgrade your software and it breaks, in docker you just go back to the previous container. It's still there and hasn't changed. If the software is on your OS directly, an uninstall and reinstall might work, but might not.
It has "Hitler bought me lunch" vibes.