A php.ini directive put into your apache conf file applies to php when it runs as an apache module (i.e. in a web page), but NOT when it runs as CLI (command-line interface).Being able to put php directives in httpd.conf and have them work on a per-directory or per-vitual host basis is just great. Now there's another aspect which might be worth being aware of:
Such feature that might be unwanted by an unhappy few, but I guess most will find it useful. As far as I'm concerned, I'm really happy that I can use open_basedir in my httpd.conf file, and it restricts the access of web users and sub-admins of my domain, but it does NOT restrict my own command-line php scripts...
