No, I think it's not the duplicate of any of the bugs you've specified.
Meanwhile I've installed to another location and it's now python 2.7.1, but the problem still present:

My configure parameters are:
--prefix=//ms/dist/python/PROJ/core/2.7.1-1/common --exec-prefix=//ms/dist/python/PROJ/core/2.7.1-1/.exec/ia32.linux.2.6.glibc.2.3 --enable-shared

The error message is:

AssertionError: '/ms/user/a/and/.local/lib/python2.7' != '/ms/user/a/and/.local/exec/lib/python2.7'

I'm executing the python interpreter from:
//ms/dist/python/PROJ/core/2.7.1/exec/bin/python

(which is the same as //ms/dist/python/PROJ/core/2.7.1-1/.exec/ia32.linux.2.6.glibc.2.3/bin/python)

In the unittest I have the following variables:
sysconfig.get_config_var('base') = '/ms/dist/python/PROJ/core/2.7.1'
sysconfig.get_config_var('userbase') = '/ms/user/a/and/.local'
sysconfig.get_path('stdlib', 'posix_prefix') = '/ms/dist/python/PROJ/core/2.7.1/lib/python2.7'
sysconfig.get_path('stdlib', 'posix_user') = '/ms/user/a/and/.local/lib/python2.7'
sysconfig.get_path('platstdlib', 'posix_prefix') = '/ms/dist/python/PROJ/core/2.7.1/exec/lib/python2.7'
sysconfig.get_path('platstdlib', 'posix_user') = '/ms/user/a/and/.local/lib/python2.7'
sysconfig.get_path('purelib', 'posix_prefix') = '/ms/dist/python/PROJ/core/2.7.1/lib/python2.7/site-packages'
sysconfig.get_path('purelib', 'posix_user') = '/ms/user/a/and/.local/lib/python2.7/site-packages'
sysconfig.get_path('platlib', 'posix_prefix') = '/ms/dist/python/PROJ/core/2.7.1/exec/lib/python2.7/site-packages'
sysconfig.get_path('platlib', 'posix_user') = '/ms/user/a/and/.local/lib/python2.7/site-packages'

I think the problem is that while get_path('platstdlib', 'posix_prefix') returns an exec-specific path different from get_path('stdlib', 'posix_prefix'), get_path('platstdlib', 'posix_user') returns the same as get_path('stdlib', 'posix_user').