The last step is just removed in PHP because of the "place files in directory" model, which is fundamentally broken and used by default. Application code shouldn't be in a place where the entire world can read it if for some reason your httpd doesn't parse it.
I totally agree that application code shouldn't be in a web-accessible directory - but that's a hosting/configuration problem, not a PHP (or even mod_php) problem. It's trivial to set up an index.php which bootstraps an application stored elsewhere on the server.
With regard to code location, I mentioned that because of Spidler's question.
1. WSGI configuration is more complicated than you make it sound
2. In your script you have to create a WSGI compliant app. Unlike PHP's quick and dirty method of spitting stdout on the webpage which is useful in making quick and dirty single file scripts
2. Yes, if quick and dirty is all you want, just use PHP, there's nothing wrong with using the right tool for the job. Personally I prefer quick and clean though, that's why I try to avoid PHP.