Just to follow up on this..
A developer with OSX El Capitan using xTools application uploader has managed to upload the very same .IPA file and it had no issues at all.
Did not get the the .app bundle error that I was getting with macOS Sierra and the application uploader.
Where you using the final released version of macOS Sierra? Which version of Xcode & Application Loader do you have installed?
Yeah, upgraded through the App store - not a Beta. App uploaded was Version 3.1 (670)
Dont use xCode.
Pretty sure you'll need to upgrade your Application Loader. Xcode 7.3.1 comes with Application Loader 3.5, and Xcode 8 has Application Loader 3.6.
My suggestion is to download Xcode 7.3.1 and use its version of Application Loader.