I would get a SAN cert and include all the required FQDNs as subject names.
Required meaning its a defined end-point for clients.If you set all the virtual directories to the same FQDN plus the virtual dierctory name, then all you need is that one subject name plus the autodiscover subject names. Also include any aliases if you use them.
You should include autodiscover.<domain> for each SMTP domain that is set as potential primary Reply address for an account.
You dont need the local hostname unless for some reason, internal users connect to that as a client endpoint.
If you are using split DNS, that would eliminate the need for the .local as a subject name.