Hi,
If in the SAN value in the certificate you have only one FQDN , you can connect to this server only with this FQDN to use Winrm over https. Because the certificate accept only once name mentioned in the SAN. It is the limitation when you choose to use auto enrollment to generate a server certificat.
If you want use another name , you have to create new computer or server certificate template in order to generate manually new certificate with the list of all server FQDN in the SAN Subject alternative Name.
The link below can help you to set the new template:
web-server-certificate-enrollment-with-san-extension.aspx
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