Multiple msixupload files for uwp with packaging project

I am trying to package a UWP application with a desktop extension as full trust process. For this, I have to use a separate packaging application for creating msixupload for store distribution and appxbundle for side loading.

My problem is that when I try to build using msbuild,

1. Multiple msixupload files are being built- One for uwp and one for the entire package. I want only one to be built for the entire package.

2. I want the name of the package to be of the UWP project to maintain consistency with what we had earlier.

I have removed all appx bundle related properties from vcxproj of UWP file except the package manifest file.

I tried setting Appxbundle property as Never in the UWP vcxproj as well.

I was able to get the packaging working using the following two solutions:

1. In the UWP app, I added:

<AppxBundle>Never</AppxBundle>
<GenerateAppxPackageOnBuild>false</GenerateAppxPackageOnBuild>
<GeneratePackageOnBuild>false</GeneratePackageOnBuild>

This stopped generating the separate package for UWP.

2. For naming, I added this to the packaging project file:

<AppxPackageName>NameOfApp_$(CustomVersion)</AppxPackageName>

and then passed the custom version while calling the build script.