I see what the problem is. In 2.x, the PythonLauncher Makefile uses 
bundlebuilder to build Python Launcher.app in Mac/PythonLauncher and 
from there it gets installed into /Applications/Python nn. Because 
bundlebuilder was removed in 3.0, r64618 checked in a copy of Python 
Launcher.app into Mac/PythonLauncher.  Later, in r68062, the build was 
changed to use a private copy of bundlebuilder so now Python 
Launcher.app is again built as in 2.x.  However, the checked-in copy of 
the app was not deleted from the svn trees and, because everything under 
the app is clobbered by the build including the .svn directories, svn 
gets upset.

The fix is easy: someone needs to svn rm Mac/PythonLauncher/Python 
Launcher.app/* from py3k and 30.  Adding Ronald to the nosy list.

So what you are doing should be fine.  Until the trees are updated, one 
way to workaround it is by making a copy of the pristine app directory 
before a build and copying it back each time you do an svn update.