I use exactly this approach with lighttpd:
Different vhosts use different fastcgi php handlers (using sockets) - and those php handlers all use different rights that fit the current vhost. My Layout is like this:
/var/www/
/vhost1/
/php/
/php-wrapper.sh
/php.ini
/webroot/
/vhost2/
/php/
/php-wrapper.sh
/php.ini
/webroot/
That allows me to have a different ini file for every vhost - with different open_basedir restrictions. Is this what you want? Yes, your integrated solution (chroot) would be even nicer, but maybe my solution can help you until there's a better way?