On my first try I had setup drupal in the web folder and that was working. But if you want to have other apps you have to create subfolders in the web folder. This way the drupal directory structure would be extended and you have to track (or worst: remember
) wich directories belong to drupal and which don't.
And if you want to setup an application which is called modules (yes I know not very likely) you are in trouble because this is an directory of drupal.