Before that moment version number was either missing or wrong, depending on what the default value was. Not good.
Suddenly realized that Info.plist is a plain text file and could be modified just right before application is created! Here's some python code:
import plistlibVery simple, even if I say so myself. In real life I use project's SVN revision number to generate a dynamic version number, but that's another story.
pl = plistlib.readPlist("Info.plist")
pl["CFBundleVersion"] = "1.1"