Install trouble with autogenerated third level domains

[sevaa]

My Cpanel based hosting setup has a feature that for every second level domain there is a set of autogenerated third level domains. E. g. if my domain is example.com, the same site also serves up autodiscover.example.com, cpanel.example.com and several others. If I want TLS on those, they need to be listed in the certificate under the SAN extension. Let's Encrypt supports that, and so does Certbot. If you specify all those domains in the run command under the -d option, comma separated but no space, the certificate is generated correctly.

As far as Cpanel is concerned, all those domains are being served up from a single site and share a certificate.

Now here is the issue. When it comes to installing the cert on Cpanel, the plugin treats all those domains as if they were separate zones and separate sites. So it tries to install the cert into example.com, then into autodiscover.example.com - and that fails, since that's not a zone from the Cpanel standpoint.

My setup also has legitimate third level domains under example.com - ones that do have a zone of their own.

Can this kind of setup can be deduced from the Cpanel API and handled accordingly?