When installing python 2.6, I used:  
   ./configure --prefix=/home/name/usr

Installation was fine and everything was installed to:
   ~/usr/lib/python2.6

But the .so files were installed to:
  ~/usr/lib/python

As ~/usr/lib/python was (no longer) declared in my PYTHONPATH, I ran
into import issues.  The problem was due to a forgotten file:
  ~/.pydistutils.cfg

So this is clearly a user error, but I wonder if it is something which
should be avoided at the setup.py level.  

When installing python, the installation locations are derived from the
results of ./configure.  When setup.py is eventually called, the
installation locations can change.  This seems undesirable.  Would it be
better if setup.py instructed distutils to ignore any configuration file
so that the installation directories matched what was used by the rest
of 'make install'?

Related:  http://bugs.python.org/issue1180