Thank you for pointing me at this. It was this way because at the time this code was written (long, long ago, somewhere just after the great dinosaur extinction if I recall well) I couldn't make any meaningful difference between the CFBundleVersion and CFBundleShortVersionString keys in the Info.plist, and Apple wasn't clear about their meaning themselves. Now everybody seems to agree that CFBundleVersion is actually a build number and CFBundleShortVersionString is the displayed app version string. The only prerequisites are that they be both in the form X.Y[.Z], equal or consecutive to their previous value, and that the pair {version number, build number} thus formed be unique.
Consequently, it makes sense to just change the CFBundleVersion key when using the automatic numbering scheme, totally. This change will be in the next version.