python3: correctly adjust include paths in sysconfigdata

This was replacing /usr/include regardless of whether it
was at the beginning of the full path (correct, when building target
python3), or in the middle of it (not correct, when building
native or nativesdk python).

Through various reasons we haven't been bitten by this until now,
but latest setuptools does expose the problem with for example
nativesdk-python3-cffi and nativesdk-python3-cryptography which both
fail without this fix.

I am not aware of anything using INCLDIRSTOMAKE, and it is harder
to adjust correctly due to the value being a list; if something
is using it, we can look at it specifically.

Signed-off-by: Alexander Kanavin <alex@linutronix.de>
Signed-off-by: Richard Purdie <richard.purdie@linuxfoundation.org>