Properly package a Desktop Bridge UWP App with a Win32 App - wpf

Question

We already have a working UWP app for x86, x64 and ARM. Everything is fine regarding store certification, all tests are passed, including with .NET native compilation.
We would like to use the Desktop Bridge (similar to what is specified here: https://blogs.msdn.microsoft.com/appconsult/2016/12/19/desktop-bridge-the-migrate-phase-invoking-a-win32-process-from-a-uwp-app/) to add a small .NET 4.6.1 WPF side-kick app to the main UWP (x86, x64) versions. The WPF app has three dependencies(x86 and x64) on some native dll's which are packaged together with the rest of the app.
We added the WPF.exe app and dll's to the existing UWP package (like specified in the above blog post - using xcopy) and built packages for HockeyApp. Locally and functionally, everything works fine for both x86 and x64. Once uploaded to the ms dev center, the Store certification unfortunately fails with the following error:
"Package acceptance validation error: Apps converted with the Desktop
Bridge and that require the .NET Native framework must be pre-compiled
by the .NET Native tool chain"
-- but native compilation is already enabled for UWP Release x86, x64.
We then tried to create a Windows Application Packaging Project (like described here: https://learn.microsoft.com/en-us/windows/uwp/porting/desktop-to-uwp-packaging-dot-net#generate-packages-for-your-desktop-bridge-app) and add both the UWP app and the WPF as dependencies. Then we created a new app manifest and store association (unfortunately it does not seem possible to reuse the existing manifest from the UWP app). We built the app store packages for (x86 x64 Release) and successfully tested everything locally. We then uploaded the package to win dev center and got again the same errors as before
"Package acceptance validation error: Apps converted with the Desktop
Bridge and that require the .NET Native framework must be pre-compiled
by the .NET Native tool chain".
As a follow up we removed the UWP project from the Windows Application Packaging Project and set the WPF app as an entry point. We then built a store package, uploaded it and the .NET native compilation error disappeared. Which is very weird...
Somehow the combination of UWP and WPF (even with native compilation enabled for UWP) causes this certification error. We have a feeling that something is wrong with the packaging.
We would really want to get this combination working or we will have to fall back to having two separate apps: one pure UWP and one packaged WPF companion app which needs to be installed separately. We truly wish we wouldn't have to do this. I'm not sure what we are doing wrong and for the moment I have run out of ideas.
PS: We also know we need to fill and submit a form regarding the restricted capability: full trust. But before we do that we need to be sure that everything else is fine.

Answer 1

UPDATE 4/21/2018
The workaround explained below is no longer needed, and in fact will not be accepted by the Store anymore. The right way to properly package a UWP app with a Win32 extension is to use the new VS Packaging Project, and then create the store package off of that project in VS. Details are in this blog post, see example #3 for this specific case:
https://blogs.windows.com/buildingapps/2017/12/04/extend-desktop-application-windows-10-features-using-new-visual-studio-application-packaging-project/#uvfV1r7937WrSkX2.97
OUTDATED ANSWER BELOW
You are hitting a known flaw in the Store ingestion process for packages that contain a mix of UWP and Desktop .NET binaries. The Store team is actively working on resolving this, so it will work automatically for submissions of this type. In the meantime you can do the following to get unblocked:
Manually create your.appxupload as follows (see screenshots for clarity below):
Go to the output folder for the AppPackage
Select the .appxsym files and the .appxbundle file
Create a new .zip file from those
Rename the .zip file to .appxupload
Resubmit to the Store with the new .appxupload file