Hi,
Its better to include all the required SAN names in the certificate for publishing of autodiscover service for the required domains.
Alternatively, Autodiscover HTTP redirect method can be configured for the other accepted domains by making use of the existing autodiscover.domain1.com. However, if configured, below pop up is expected in the outlook clients.
Reference: http://techgenix.com/using-autodiscover-large-numbers-accepted-domains-part1/
Please Note: Since the web site is not hosted by Microsoft, the link may change without notice. Microsoft does not guarantee the accuracy of this information.