I managet to get it working per virtual host with this wrapper (I also came up to the idea that it has to be chowned to root/wheel ):
I reworked your wrapper to look like this:
The PWD has to be exported to hide the path.
# This will fake the name & path and hide the /usr/local/cpanel/cgi-sys/php5 path!
export PHPRC=`dirname $PATH_TRANSLATED`/php.ini
I prefer to use the PHPRC, because it will just look in the specified directory for php.ini, because with the '-c' you have to first check does the files exists (as you do in your example).