That could be related to the Lego version you have installed. Could you please let us know which version are you using running the command below?
sudo /usr/local/bin/lego --version
Also, could you please let us know if you are using the
generate-certificate.sh script or the Alternative approach guide? As you ask for the step number 3, I understand you are using the alternative approach, but please confirm us.
Apart from that, it is not necesary to modify the
/opt/bitnami/apache2/conf/ files as after following the steps, the files
/opt/bitnami/apache2/conf/server.key are not real files, but symbolic links to the files generated by Let's Encrypt.