You'll have to change /root/ispconfig/isp/conf/vhost.conf.master template file. Change all .html to .php for error pages. Plus you'll have to change template files for actuall error pages. Maybe also make_vhosts() function
Not sure about this but be aware that if you have a site that has disabled php scripts that it might also affect error pages for that site. <--- Not sure if this is true or not! Would kinda make sense..