The problem is all the legacy applications which are a mess of random PHP files and rely on the web server itself to dispatch requests based on the path of the file - in this case any PHP file can get executed if it happens to be in a location served by the web server. Rather than disallowing PHP execution in select folders, how about allowing PHP execution only for specific paths - those that you expect incoming requests to hit? That way no malicious code can run unless it manages to overwrite an existing file.