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.