I'm having similar problem with distutils.
http://mail.python.org/pipermail/python-dev/2008-November/083670.html

Is there any reason customize_compiler 
- only get CPPFLAGS in env, not ones from sysconfig?
- doesn't get OPT from from sysconfig, but it's used when env has CFLAGS?

I think this is a bug.
CPPFLAGS and OPT both should be used when building extension modules.
Just imagine a system that has include files in a non-standard locations
and explicitly added -I compiler flags to CPPFLAGS to adjust it.
When building an extension modules, the system should requires
the same CPPFLAGS settings. Without it, it won't compile.

In my opinion, this is rather serious bug.
So it would be nice to fix this before releasing Python 3.0/2.6.1/2.5.3