If those websites are on the same server, and you just want to limit the resources for each virtual host, you can consider CloudLinux system or a feature like
cgroups. If you want to run the PHP per virtual host user, try
suEXEC for each external app on the virtual host level, if you want to sandbox the whole data for each VH, try
namespaces. Those features should have nothing to do with PHP handlers like php-fpm or PHP LSAPI.