Hi.
We used luebbybaer's solution at first because we were catching a deadline, but it seems there is an easier way to solve it.
If you have downloaded apple/unityplugins repo from github, you can go to plug-ins/Apple.Core/Native and open the AppleCoreNative.xcodeproj. Then select the AppleCoreNative project, go to Build Setting and search for Packaging and set the Generate Info.plist File to No. This will make it so that during packaging phase it actually takes the Info.plist file that is included in the AppleCoreNative folder and already has the CFBundleShortVersionString key set.
Then you can just run the build.py command as before, and import the newly generated tarball packages back to Unity.