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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.