I agree with Eric's comment about why have shebang lines at all for files in the standard library.  There isn't any use case or recommendation for ever putting /path/to/lib/pythonx.x or its subdirectories directly on a shell search path is there?

WRT the three files found in the Mac directory, I think all of these should be left alone for right now.  Specifically:

Mac/BuildScript/build-installer.py
   is the script used to build OS X installer images; at the moment, it depends on a system Python 2 as a build tool, primarily because of Sphinx, and there has been an effort to keep the Python 2 and Python 3 versions of the script in sync.  Eventually that will need to be changed.  The shebang line could simply be removed.

Mac/Tools/fixapplepython23.py:
    this one needs to be looked at a bit more as it runs during the installation process but only on OS X 10.3, a minor and dwindling niche of the user base.  I think that it actually depends on the Apple-installed system Python at run time.  I'll follow up on it.

Mac/Tools/bundlebuilder.py: #! /usr/bin/env python
    AFAIK, bundlebuilder is neither used during the build process of Python 3 nor is it installed.  It is used in the Python 2 build process.