Where the website files could be located?
This is partly covered under the FHS for Linux. http://www.pathname.com/fhs/
/home/user/* is really only appropriate when a single account on the system is going to be modifying content.
Other shared locations like /var/www/vhosts and /srv/www are more appropriate when many users will be modifying content.
It is not entirely uncommon to have the content exist in one of those shared locations and have symlinks to or from the users home directory.