Cpanel httpd.conf vs domain mapping

Generally having each user who has their own domain name be able to have their own cpanel username/password so they can manage email is important to the end user.

Utilizing 3rd party toolsets leaves a lot to be desired - especially from a cost perspective.

Furthermore tools such as Google Apps (gmail) ends up having customers be marketed by Google for other products like google sites.

What I would love is the ability to, when we add a site into multisite using the Domain mapping for the httpd.conf to be updated in tandem with the whmcs plugin perhaps (or manual even) and have that entry distilled via the cpanel system so it does not change in the future.

This would allow for us to have each user be given their own user/pass for setting up email accounts but using the multisite install as intended