Website specific php settings are avalable for fastcgi in ISPConfig 3, so there is no need to use mod_php for a website at all and its also quite insecure. The security that you think to add by using folder specific php settings are completely lost by the use of mod_php, so at the end your site is more insecure.
1) Change php mode of the website to fastcgi
2) Enable the suexec checkbox in the website settings.
3) Set the php options that you want to have for this specific website in the custom php.ini field on the options tab of the website settings.
4) Install joomla.