This is by (Windows's) design - separate apps are treated as separate by the Windows app model. In the latest and N-1 updates to Windows, the AppData redirection only applies to newly created files, not those that already exist. [1] Before then, it used copy-on-write.

The design is based on having seen many apps break because of inadvertently sharing data, and also apps failing to clean up after themselves well (of which Python is *very* guilty). The built-in "Reset App" and "Uninstall App" functions would not be viable without this separation.

What it really means for apps that are trying to share state across different Python runtimes is that they're not going to have such a great time. The best option I can offer is to use the user's Documents folder instead, which is explicitly shared (though may also be synced between machines, so not always appropriate).

The next best option is to recommend that the Store package only be used on its own, and not in conjunction with other Python installs. Those who need multiple versions or mostly-but-not-quite-separate installs will need to use the traditional installer.

But what it means for all the other tools that write to AppData is that they don't have to worry about old settings laying around or causing additional clutter. The standard "Reset app" action is a viable way to fix issues in configuration or cached files (and uninstall all packages). From a user point of view, I really like these features.

1: https://docs.microsoft.com/windows/msix/desktop/desktop-to-uwp-behind-the-scenes