cPanel subdomains for domain alias

Hi, I am hoping someone can help me here. I have shared reseller hosting with a supplier and one of my accounts has two domain aliases. The primary domain in this account has the cPanel subdomains for cpanel, whm, webmail, webdisk, cpcontacts, cpcalendars etc. The autoSSL facility via Lets Encrypt will install a cert for these subdomains without a wildcard. However the two domain aliases dont get the subdomains for cpanel etc. the DNS Zone editor shows the subdomain A records for each of the domains as well as the primary domain but I cannot get it to assign the SSL cert for these subdomains, therefore while i can get to