I do not agree with this statement
Look, Apache process (namely httpd) needs an access to its files out of the web tree,
php module, namely libphp4.so needs an access to the files out of the web tree.
Without letting them access their files out of the web tree, you will not get them working at all.
On the other hand, if your system has php files to be included from the out of web tree, how would such environment be abused?
Quite the opposite, if you put to the web a script that does not make precautions on its input, you'll make risk much higher.
That's why, for example, PEAR scripts are always installed out of the web.
It's
the way people are improving security.