ConsentDev,
I was able to successfully upload to the store after much trial and error ( partially due to using Adobe Air and Windows compile with hand off to Mac for final upload). Here is my process:
1. I would download a zip file created by another person (Windows) via ftp.
2. Close ftp ( and in my case I closed everything ) and uncompress via Finder.
3. Discard download and Compress "Payload" via finder.
4. Rename the ".zip" file to ".ipa" which would would bring up the prompt "are you sure you want .ipa?" (file will then take on iTunes icon).
5. Launch "Application Loader" without using Xcode ( I use Spotlight and type in "Application Loader" ).
6. Load the file and follow the steps of "Application Loader"
I finished with one warning that I was already aware of ( integer via .plist ) that is an Adobe Air issue and they are on that.
My upload was successful with the warning and now awaiting confirmation from Apple to test on my device.
I stayed in latest build of Xcode / Sierra and Application Loader ( at one point was going to go to another computer and earlier version of Xcode ).
I would launch Terminal and test my file via that which helped me double check to make sure Application Loader error messages were correct.
Use the reports to help decipher issues and I hope this helped.
The main issue was "missing directory" so my uncompressing / recompressing and renaming would somehow remedy the issue.
Also side note several days ago I would have to create a folder which I named .ipa then put Payload and contents in there then zip.
So if all else fails try both ways and make sure to do it from Finder as I was renaming inside my FTP program which would give errors on the upload.