I wanted to use both a mobile and desktop domain for my main site of a multisite network. (www.bradbrownmagic.com accesses the desktop version, and m.bradbrownmagic.com accesses the mobile version.) After some trial and error, I came up with something that seems to work for my needs.
I'm using an up to date WordPress install: WP 3.1.2, MU Domain Mapping 0.5.4, and WP Mobile Pack 1.2.4.
Here's what I did:
Under Network Admin > Settings > Domain Mapping, check the box for "Disable primary domain check."
Under Network Admin > Settings > Domains, create the alias. It won't let you create an alias for the main site, so create it for anything else. I used 7 for the site ID, as that was not being used. I also had "primary" unchecked, though I don't know that it matters since primary domains are disabled anyway.
I had to manually edit the database to point my new alias to the main site. Using phpMyAdmin, I edited the wp_domain_mapping table. I updated the record for my alias and changed the blog_id to 1, for the main site.
Under Site Admin (for my main domain) > Appearance > Mobile Switcher, I set it up to use my mobile and desktop domains.
That's it. Since I had to turn off the primary domain functionality for the entire network, I also updated my .htaccess to do a rewrite for the non canonical domains in the network to prevent the possibility of duplicate content issues.
Obviously, this is a hack, so if you decide to give it a try, back everything up and proceed at your own risk!