This has always (well... since secure certificates for everything became a thing) been my argument against "pointers" or "domain aliases" and just treat every domain name as an "addon" domain with it's own VirtualHost container.
It makes the issuance of secure certificates easier and that much more straightforward.
By having multiple domain names attached to the SANs of a certificate then the automated process that renews the certificate is going to have to figure out which of the domain names resolves to the server before that issuance, because the domains that no longer resolve to the server will fail DCV for the certificate and if one fails, then the certificate will not get issued.
If an "addon" domain has it's own VirtualHost container - but shares the DocumentRoot with another domain - this effectively becomes a "pointer" or "domain alias" with the caveat that it has it's own secure certificate. If that domain stops resolving to the server (for whatever reason) that certificate is just skipped when it comes time to renew it. It's resolution status has no bearing on the certificates for the other domain names (with their own VirtualHost) on the account or "pointing" to the same DocumentRoot.