The original backup created uses the app’s built-in auto generated templates & images. At this point, the app has ownership of your layouts so it doesn’t need to include those files in the HRP. By saving the file with the Designer you’ve taken complete ownership of the layouts. It creates clones of all those built-in XAML files & copies them to the Pages directory of the HRP so they can be customized by you. Those XAML files & images are not included in the original app backups because you are using the “built-in” layouts & images at that point.
Once you’ve saved a HRP with the Designer it has to assume that you may make custom changes to the XAML files. Those files cannot be changed in the apps themselves and that’s why they don’t need to be saved in your original app backup.
From time to time the built-in templates & images are updated. Since you’ve chosen to use the Designer, you will no longer automatically receive those updates in the apps. If you want to update your XAML templates to the latest version you will now have to right-click the Pages folder in the Designer & select “Synchronize Templates”. This will overwrite your XAML files with the latest “built-in” layouts.
So you really need to consider which is best for you. Don’t use the Designer just to link Devices or organize Groups. You should only use the Designer if you plan making custom changes to the XAML files.