For certs created by nodes, we don't want the nodes being able to control what SANs are used. In the same way we scope the cert DNs at the CA level, we could specify SANs at the CA. We could use a whitelist of domains and we could support a list of SANs that are set for all certs signed by that CA.
For example, creating or editing a CA with --san-required 'www.mydomain.com' and --san-optional '*.us.mydomain.com' would force all certs to have a SAN of 'www.mydomain.com' and optionally something below 'us.mydomain.com'.