No, just because a site allows users to upload files doesn't mean they can replace the top-level index.php, for if that were true then whoever setup that server

No, just because a site allows users to upload files doesn't mean they can replace the top-level index.php, for if that were true then whoever setup that server needs to look for job opportunities in the circus. The problem with removing the PHP handler from all other writable directories is the reality of dealing with many 3rd party modules, themes, and apps that have their own upload directories, and sure you can audit all 3rd party code and rewrite it yourself, but you should also assume the code is full of holes anyway and configure the other layers in your stack according to the principle of least privilege.