I'm have a similar issue with my multisite installation. Main site is revision1design.com and right now I only have 2 sites but planning on more. I want it when you subscribe to each site that the blog URL in the confirmation email is the mapped domain so for my site; ThePodcast.ca, it will show up as http://www.thepodcast.ca in the email not thepodcast.revision1design.com.
And this would be what I would want for each site after, can you explain how to do this, through searching I've seen the issue resolved by others but never explained.