I am trying to set up PHP sessions for suPHP (see here). I need to have my php validation file owned by the user so that when suPHP kicks in, it will do so for the correct u
There are quite a few configuration options for suPHP, and without them I can't give an exact answer, so I'll assume that you are running a pretty std configuration, because if you don't have it set up pretty strictly then you introduce so many exploitable holes that there isn't much point in using it.
This is part of the formal assurance model of suPHP and if you want to change it, then don't use suPHP.
The user can define his/her own path for loading PHP.ini. By default the user can specify a custom php.ini and IIRC you can't disable the suPHP_ConfigPath option. After all at the end of the day, you are running php-cgi in the users UID. So this mean that even if you establish an auto_prepend_file (which could be owned by root and not writeable by the UID) then the knowledgeable user could still bypass this.
My simple Q is why are you using PHP, or at least the suPHP established PHP handler to do what you are trying to achieve here? Keep PHP for the user and user privileged functions. Use a CGI script or even a RewriteMap and a prg: option for these "systemy" functions. You could even trivially implement this in PHP if this is your preferred language as this would be executed using php-cli. There are lots of tutorials on how to write Map prg functions. They're pretty easy to implement.