Email addresses contain @HOSTNAME.domain.com when mail is configured using Profile Manager
Another update...  I started fresh with a new install of Lion.  Updated to 10.7.3 first, having read about everyone's nightmares after this update.  

Anyway, my Kerberos realm is now set to domain1.com, but Profile Manager still insists on using the incoming server name (hostname.domain1.com)as the email address.  I tried using both variables, %email% and %short_name%@domain1.com.  No luck either way.

What I find aggravating is that if you view the Profile when it is installed, or in Systems Settings > Profiles, the email address is correct.  This was also the case before I started over.  This leads me to believe that the profiles are somehow not implemented correctly by either Mail or the profile installation process.  I looked at the XML in the profile, and do not see any settings that would be responsible for the behavior.  Everywhere I used a variable, the resulting values were precisely as I expected.  

I again tested the default "Settings for Everyone" profile that is configured automatically based on your server settings, and the Server Admin > Mail > General > "Host name:" setting still takes precedence.  So, if you put your actual hostname in this field (i.e. mail.domain.com) your users will all end up using user@mail.domain.com as an address. 

I am admitting defeat for now, and just set up A records for domain.com that point to the mail server.  This way, I can set my two profiles up, one for each that use domain1.com and domain2.com, respectively, as their incoming servers.  The email address will then default to %short_name%@incomingserver