(I think?) that is ok. Let me lay this out, please tell me if it makes sense:
1. Edit the URL settings in the user's site to state that the URL is http://username.com
2. At the user's registrar, set the DNS to where my multisite network is hosted. My multisite needs to be on a dedicated IP address.
3. Make sure cookies are handled correctly.
4. Random internet surfers can now put www.username.com into their browser and they will end up at the user's site correctly, and all URLs will be re-written to domain base username.com
5. (this one I am really not sure about) When user wants to log into their WP back-end at their site, they'd still use the link username.foonetwork.com/wp-login.php (?)