I created a simple project to upload to help out a user in another thread. I used "Export As Zip" with option "Include Shared Modules" as it was the only option available. I tested the zip file and it has duplicate AndroidManifest.xml and icon.png files. This is the first time I've used Export as Zip so I don't know if it's version (v4.3) related.
The project is attached.
The project is attached.