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 tools like Advanced Installer to do it for you.
To understand more about MSIX and how files outside of the installation path can be managed I recommend this article/presentation I wrote last month.