Have you updated the config.json file inside /opt/r3/` to point to the new certificate & key files (web->cert/key)? You probably also want to update the port to something other than 80 (web->port).
The config file is read during service start so you need to reboot your container after changing it.
You also need to reconfigure parts of the Docker file:
EXPOSE 80
CMD ["/opt/r3/r3", "-run", "-http", "-config", "/opt/r3/data/config.json"]
You need to expose the port you have chosen inside the config file. You would also need to remove the -http argument.
The default Docker compose file also maps port 80 by default. You need to update this as well.