Why does the Windows Store modifies the app package?

Question

I'm building a WPF application and I'm using Xaml Islands to add Windows 10 look and feel to the app. I'd like to use the Lottie library to play Adobe After Effects animations. Everything works fine until now.

When packaging the desktop bridge project, I receive an App manifest validation error. This issue appears on multiple places, and it seems that Microsoft won't fix it. Here, here, here, also here, etc. From this workaround, I added the following lines to the wap project:

<Target Name="_RemoveWinMDFromAppxManifest" BeforeTargets="_GenerateCurrentProjectAppxManifest">
    <ItemGroup>
      <_AppxWinmdFilesToHarvest Remove="@(_AppxWinmdFilesToHarvest)" />
    </ItemGroup>
  </Target>

With this, I could achieve to not to duplicate some dependencies in the AppxManifest.xaml when creating the build, so the issue has gone and I could create the package for the Store submission.

I could upload to the store, it is published, but when I install it from the store, the app crashes when it should display a lottie animation with the following exception:

* When the Lottie is initalized from Xaml:
(0x80004005): Error HRESULT E_FAIL has been returned from a call to a COM component.
   at Windows.UI.Xaml.UIElement.Measure(Size availableSize)
   at Microsoft.Toolkit.Uwp.UI.Controls.WrapPanel.MeasureOverride(Size availableSize)

* Exception, when it is initialized from the code behind:
Cannot create instance of type 'Microsoft.Toolkit.Uwp.UI.Lottie.LottieVisualSource' [Line: 0 Position: 0]

The interesting part is that the animation is played when I install the exact same build from the local package. So the Store modifies the package during the publish procedure?

I would appreciate any ideas. What else can I do with the App manifest validation error to create the package? Can I remove the duplicate entries some other way from the AppxManifest during the build process? What can I do to make it work when it is installed from the Store?