Exactly, you can make 99% of changes from a Scoped App to any Global elements. There are a few exceptions, but usually it just requires a Cross-Scope Access record then the Scoped App can get to what it needs.
For data records that you add and want to be part of the application, you have to click the check box from a list view, then on the drop down action, select Create Application File. It will create an appropriate record in the application that can move forward on Install, Install and Upgrade, or only as Demo Data. So this can even store your configuration values and such.
Scoped Apps also allow you to create system properties and property categories and it will generate a Configuration Navigator Module for you where you can have a page of property values like store apps do.
Aoife
