The Apache request-handling chain is much richer than simply passing off incoming requests to a CGI or PHP script. Using mod_{perl,python,ruby,etc.}, you can implement authenticators, URL-rewriting modules, log handlers, output filters, etc., and take advantage of the mature Apache infrastructure for such code.
Basically, if you want to be able to slice and dice HTTP requests at every stage of processing, not just the content-generation one, the Apache mod_* add-ons are a pretty powerful tool for doing just that.