This is actually a requirement of PEAR, not PHP:
[adrianp /usr/pkgsrc/lang/pear ]$ cat MESSAGE
===========================================================================
$NetBSD: MESSAGE,v 1.1.1.1 2007/05/05 21:21:45 adrianp Exp $
In order to use PEAR packages you may want to alter the default
include_path of PHP to include the PEAR installation directory where the
packages are located. To do this you need to edit the include_path
directive in your php.ini file:
${PKG_SYSCONFDIR}/php.ini
Change the "include_path" directive to read as follows:
include_path = ".:${PREFIX}/lib/php"
===========================================================================
[adrianp /usr/pkgsrc/lang/pear ]$
In pkgsrc land we tend not to modify installed configuration files. In this
case php.ini is already installed from the php package so the pear package
just spits out this message.