I think you're being awfully generous in suggesting that "the PHP community" has moved away from the everything-in-one-file method. Outside of some big projects like Drupal and work being done by some elite coders, I think most PHP scripts still mash it all together. From what I see, although there are still plenty of CGI/HTML scripts out there, Perl is way ahead in that regard.
That ability to toss a little code into an HTML file is what made PHP popular, after all. You didn't have to deal with file permissions or any of the stuff that made CGIs tricky at times; just stick your code in the page. That method makes large projects nearly impossible -- systems like Drupal and Wordpress are a mess, even with separation of code and layout -- but it makes the quick-and-dirty stuff quick. Take that away, and you're left with what, about a thousand inconsistently named functions?
Available for small or large Perl jobs; see my home node.