Actually we do tend to modify installed config to match the paths used by pkgsrc :) I think this is one case where it makes sense to have the default php.ini include the pear path. What do others feel?
Usually I read the "make info" pages, but in this particular case, PEAR wasn't installed by me and I really wondered why PHP wouldn't find PEAR automagically by itself. It only came very late to my mind that php.ini was lacking something, for something I took granted.
So, yes, have the PEAR-package alter the php.ini, please. -- Markus Illenseer