I think Trey needs to push back - *IF* I understand him correctly, it sounds like duplicate websites, but running as different users. That, to me, literally makes no sense...mmmm, unless a) the source of the request doesn't understand what he wants, or b) there's something illegal going on, and users going to a different site have different things happening, based on data/database content.
The way I interpreted it he want's it setup so each domain (example1.com, example2.com, etc) to each runs it's own Apache server under an unprivileged login (apache1, apache2, etc). Chroot's should accomplish that easy enough. He then wants to use the same CMS (Joomla, Wordpress, etc) on each site. My assumption is he's hosting several CMS sites and want's each isolated so a compromise of one won't compromise the others.
What is confusing is what he means by 'codebase?' Does he want each chroot to have it's own independent copy? Or does he want to share the CMS core files across all instances?