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I assume that the Python directory layout is the same on all
currently supported platforms by Python. I really don't know
enough to be sure - the less that's true, the less my
following argument will be valid:

There are really two concerns:
1) make Python conform to the FHS
2) make Python behave the same cross-platform (Windows,
Unix, Mac, BeOS, OS/2, VMS, AS/400, ...)

You can't have both unless you force the FHS directory
layout onto all other platforms. I personally think that 2)
is a good thing.

I welcome the proposal of a configuration option to make
Python FHS-compliant, but I think it should not be the
default. Btw. you'd probably have to patch distutils, too.

Jack said that Pyhon include files should be cross-platform.
AFAIK they are, with one exceptions: pyconfig.h.