Can I make a sugestion?
I see the folder layout / domains as a single issue which shouldn't be too hard to solve.
Now the domains are under a different tab and you can link domains to that folder (symbollic links) quick note: I would not put these in the same directory / file system eg: /home/user_name/website.tld -> /home/user_name/folder.
A nice way for this to work imo would be for a seperate folder to have all the symbollic links. I use /etc/httpd/vhlinks/ which maps the web address to a folder.
This brings me to the virtual hosts. I think a good feature would be to use mod_vhost_alias in apache. By using virtualhost "Templates" you would reduce your memory footprint, and also remove the need to restart the webserver every time you add a domain.
I am planning on implimenting mod_vhost_alias for my own network, and am happy to submit this code back, would be interested in hearing some feedback on what everyone thinks about what i've described there.