Ordinarily, your site's document root (as seen by Apache) is /home/public. If you enable the per-alias document root feature from the site info panel in our member interface, the alias being used will be added to the site's document root.
For example, if you have www.example.com configured as an alias for your site, then when someone visits it Apache will treat /home/public/www.example.com/ as the document root. If you also have the alias other.example.com added to the site, then requests using that alias will be directed to /home/public/other.example.com/.
If no directory exists for a given alias, all requests for that alias will return 404. If a directory exists but no alias has been added in our UI, it will not be recognized as an alias.
This feature can be very helpful if you have multiple sites that need to share some but not all of their data, or if you have several sites with different content that are all based on a common framework. Using this feature can allow you to maintain one copy of the framework.
This feature is not a substitute for creating multiple sites. With this feature, one site is still just one site. There is no additional security, isolation, or protection implied by using this feature. Just as there is nothing protecting http://www.example.com/one/ from the contents of http://www.example.com/two/, there is nothing between http://one.example.com/ and http://two.example.com/ if they are pointed to the same site by this feature.