I specify in setup.py the following include_dirs and library_dirs: 
/opt/x86_64-sdk-linux/usr/bin/python3 setup.py build_ext \
--include-dirs=/opt/neon-poky-linux-gnueabi/usr/include/python3.5m/ \
--library-dirs=/opt/neon-poky-linux-gnueabi/usr/lib/ \
--rpath=/opt/neon-poky-linux-gnueabi/usr/lib/ \
--plat-name=linux_armv7l
However, the generated gcc commands (when executing python3 setup.py build_ext) also include the include path where python3 is running from (I have added newlines for readability):
arm-poky-linux-gnueabi-gcc \
--sysroot=/opt/neon-poky-linux-gnueabi \
-I. \
-I/opt/neon-poky-linux-gnueabi/usr/include/python3.5m/ \
-I/opt/x86_64-sdk-linux/usr/include/python3.5m \
-c py/constraint.cpp -o build/temp.linux-x86_64-3.5/py/constraint.o
The third include path was not specified explicitly, but is still used when compiling.
How would I go about ensuring only the include-dirs I specify are being used?
You will need to override build_ext command because the stdlib's build_ext ensures the Python header files, both platform specific and not, are always appended to the include paths.
Here's an example of custom build_ext command that cleans up the include paths after the options are finalized:
# setup.py
from distutils import sysconfig
from setuptools import setup
from setuptools.command.build_ext import build_ext as build_ext_orig
class build_ext(build_ext_orig):
    def finalize_options(self):
        super().finalize_options()
        py_include = sysconfig.get_python_inc()
        plat_py_include = sysconfig.get_python_inc(plat_specific=1)
        for path in (py_include, plat_py_include, ):
            for _ in range(self.include_dirs.count(path)):
                self.include_dirs.remove(path)
setup(
    ...,
    cmdclass={'build_ext': build_ext},
)
Same approach for library dirs: clean the list when options are finalized:
class build_ext(build_ext_orig):
    def finalize_options(self):
        super().finalize_options()
        ...
        libdir = sysconfig.get_config_var('LIBDIR')
        for _ in range(self.library_dirs.count(libdir)):
            self.library_dirs.remove(libdir)
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