Nit: a CN (stored in the Subject field of a cert) is not an FQDN, though historically web browsers treated them as such. This practice is now deprecated. Modern practice is for the domain name(s) to be placed in the Subject Alternative Name (SAN) field.
The Subject field is not consulted so long as the SAN field is present, and can in theory be any X.500 Distinguished Name, of which Common Name is one possible attribute, which may be any freeform string of a limited length (though it is typically set to the primary domain the cert is issued for, for easy identification).