At SunSITE.dk we host many different projects which some of use PHP. These seperate projects each want to use their own prepend directives, and some we want to be more strict on than other. etc. This results in <Directory> directives like this:

<Directory /mnt/www-docs/www-docs/php-share/phorum>
php_admin_flag safe_mode on
php_admin_value open_basedir .:/pack/apache/local/php-safe/phorum/conf
php_admin_flag sql_safe_mode off
</Directory>
etc.

The problem is that we had periodic faults where directives for f.eks.
/lgdc/ would apply themselves to our document root and other sub projects. Like the configuration "overflowed" from subdirectory. As it is a periodic problem it is hard to reproduce, but we stopped this behaviour by adding a <Directory> directive for /mnt/www-docs/.

It seems like the configuration which are applied to the php engine in one apache process are not reset if there is no other directive for the new dir.