From my experience, the wizard never generates up-to-date contents, so I never use it.
Moreover, there are likely files that are only relevant at the top-level (e.g. gitattributes, gitignore, settings.gradle.kts, the gradle wrapper dir, etc.), and thus wouldn't be relevant for a sub-project of an existing project. (EDIT: sorry I missed the fact that your project is currently empty and you would like to generate top-level stuff).
What's the list of files you're actually interested in generating?