This is not going to be possible.
Plesk is hardcoded to write the httpd.include in a specific format, and that format includes the use of httpdocs as the root of the site.
As an alternative solution, perhaps removing the httpdocs folder and creating a symlink to the location you want to use instead (so if you want to have www in the root of the domain directory /var/www/domain.com/www and then create a symlink from www to httpdocs). Just make sure you sort out the permissions and ownership of the symlink, otherwise things break.
Good luck.