Once an Application's theme is setup, along with the layouts, menu, header, footer, Login page, etc, it should be possible to create a module to be used as template for all New Modules created in this Application.

Otherwise, for every new module, we need to go in and delete the Common flow, the Menu related static entities, the theme, then add the Application theme reference and do any other customizations (User Provider, anything Application specific).

Because of this, it's most often better to create a Blank Module and do this setup manually.