The vendor folder is not a resource root. A resource root is a folder where resources such as images and scripts will be served from by the web server.
In your case the only folder that should be marked as a resource root is probably the web folder, but ironically, is almost the only one you haven’t selected as a resource root. Marking web as the resource root means that the absolute URLs /css/foo.css and /images/foo.jpg could be valid resources served by the web server; you probably want to remove all other folders from resource roots.
It is correct to exclude the vendor folder because it is not part of your first-party project code. In order for code completion to work for third-party code you must add the vendor folder as an external library. This can be done by navigating to Languages & Frameworks > PHP in the options and specifying the vendor folder as an include path.