I think you have to save both autodiscover settings in your DNS Server.
If a userr authenticated to Active Directory the mail adress is used to generate the autodiscover entry whicht is lookup in DNS. But I think that it is a goof Idee to save the Serrvicerecord autodiscover entries in DNS
_autodiscover._tcp.domain TCP 443 Hostname of your Exchangesever
So you can have one Exchangeserver with multiple maildomains and the certificate of your Exchangeserver only contains the name of the server and not the autodiscoverr.domain names with doesn´t fit on big organisations with a lot of maildomains.
regards Thomas Paetzold visit my blog on: http://sus42.wordpress.com