Well, googling /usr/local/cpanel/3rdparty/etc/php.ini is a heckuva place to start, since it comes up with numerous discussions, most of them pertaining to problems in /usr/local/cpanel/3rdparty/etc/php.ini with Fantastico installation (as Fantastico uses cPanels internal PHP to install).
Well, one could extrapolate that cpanel has its own internal PHP for add ons and third party installs and itself precisely because it needs to use wider variables and looser permissions than would be recommended on a server for normal PHP processing (example - turn off shell_exec in there and see how far Fantastico gets when installing).