Aliasing a subdomain on a wordpress network

So far as we know, we can control the subdomain by the WordPress subdomain network and apache rewrite rule(nginx works too.).

The subdomain is a rule, so you can’t set it directyly in .htaccess by using your http://www.supercooldomain.com, but you can set another apacahe virutal host use your cooldomain. There is another wordpress plugin may can help you.
http://wordpress.org/plugins/wordpress-mu-domain-mapping/