I knew that most Citrix components work with SAN certificates, as per the eDocs at http://support.citrix.com/proddocs/topic/xmob-deployment/xmob-deploy-certificates-con.html. However when installing my first site that wanted to use a SAN certificate for their XenMobile Device Manager server, it would not accept the SAN certificate during the setup process.
Note in the above screenshot, the certificate and password are accepted but you cannot click Next, and the FQDN and other details are not picked up from the certificate.
There is an easy way round this however, instead complete your XenMobile install using the self signed certificate that gets generated during the install. Then swap the self-signed certificate for your SAN certificate by following this excellent post from Port25Guy:
Once you have followed the above instructions and restarted the XenMobile service, the console should be accessible, and devices able to communicate with the XDM server and enroll etc using the SAN certificate without complaints.