Notice that if you want to use VPL and Apache at the same machine and Apache is using Certbot to get the SSL certificates the correct way to install VPL is to indicate that you already have certificates and using symbolic links or the SSL_CERT_FILE and SSL_KEY_FILE parameters to allow VPL to get access to the certificates got by Apache.
I guess that if you are getting two different certificates for the same HOSTFQDN the Certbot generates two different directories.
If you are using Apache on the default ports HTTP:80/HTTPS:443 you must set VPL on two different ports g.e. HTTP:8080/HTTPS:8081. You can also remove the HTTP port from VPL.