The installation path of an MSIX package cannot be changed.All the files you have included in your package are installed inside an app-specific folder under"C:\Program Files\WindowsApps<your app>\".
This is a design decision from Microsoft. Only for MSI/EXE installers you can change the install path.
If you want to add files in other folders too, you need to copy them the first time your application is launched. For that, you have multiple options. You can write your own code inside your application to copy the files in other folders or you can use third-party MSIX packaging tools to help you do it.