How does the application act when not packaged and the intentional crash happens? That is how you should expect the application to run.
A packaged application not set to run inside an appcontainer has the same rights and almost the same environment as the application running without the package. One set to run inside an appcontainer has a lower integrity level but still almost the same environment. Understanding how packaged desktop apps run on Windows gives a description of how packaged applications run, and it does not state that an application running inside a package is unable to mutate the Windows OS state.
The previous text ignores Windows 11 24H2's updates which changes things a little, but even that doesn't prevent mutations to the OS state.