Just pointing out for other users: Yes, the steps in these docs are needed, but the
generate-certificate.sh script does not support to generate multiple certificates for the subsites. The "Alternative Approach" below must be followed instead, as it allows having multiple certificates simultaneously.
As you mention, this would create a conflict with the main domain certificate. You could just use any other file name, e.g. the domain name:
sudo ln -s /etc/lego/certificates/**DOMAIN**.key /opt/bitnami/apache2/conf/**DOMAIN**.key
sudo ln -s /etc/lego/certificates/**DOMAIN**.crt /opt/bitnami/apache2/conf/**DOMAIN**.crt
Then, following this section, just take into account that the
SSLCertificateKeyFile directives in the VirtualHost for this domain must point to the correct path: