Well, cross compiling extension modules already works fine...

$ _PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_m_linux_aarch64-linux-android PYTHONHOME=~/Projects/python3-android/build/21-aarch64-linux-android-4.9/usr python3.7 setup.py build_ext
running build_ext
building 'xx' extension
creating build
creating build/temp.linux-x86_64-3.7
/opt/android-ndk/toolchains/llvm/prebuilt/linux-x86_64/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -target aarch64-none-linux-android -gcc-toolchain /opt/android-ndk/toolchains/aarch64-linux-android-4.9/prebuilt/linux-x86_64 --sysroot=/opt/android-ndk/platforms/android-21/arch-arm64/usr -fPIE -fno-integrated-as -target aarch64-none-linux-android -gcc-toolchain /opt/android-ndk/toolchains/aarch64-linux-android-4.9/prebuilt/linux-x86_64 --sysroot=/opt/android-ndk/platforms/android-21/arch-arm64/usr -fPIE -fno-integrated-as -fPIC -I/home/yen/Projects/python3-android/build/21-aarch64-linux-android-4.9/usr/include/python3.7m -c xxmodule.c -o build/temp.linux-x86_64-3.7/xxmodule.o
creating build/lib.linux-x86_64-3.7
/opt/android-ndk/toolchains/llvm/prebuilt/linux-x86_64/bin/clang -shared -target aarch64-none-linux-android -gcc-toolchain /opt/android-ndk/toolchains/aarch64-linux-android-4.9/prebuilt/linux-x86_64 --sysroot=/opt/android-ndk/platforms/android-21/arch-arm64/usr -pie -L/home/yen/Projects/python3-android/build/21-aarch64-linux-android-4.9/usr/lib -target aarch64-none-linux-android -gcc-toolchain /opt/android-ndk/toolchains/aarch64-linux-android-4.9/prebuilt/linux-x86_64 --sysroot=/opt/android-ndk/platforms/android-21/arch-arm64/usr -pie -L/home/yen/Projects/python3-android/build/21-aarch64-linux-android-4.9/usr/lib build/temp.linux-x86_64-3.7/xxmodule.o -o build/lib.linux-x86_64-3.7/xx.cpython-37m-aarch64-linux-android.so
clang: warning: argument unused during compilation: '-pie'
clang: warning: argument unused during compilation: '-pie'

And it's running fine, too:

$ adb push build/lib.linux-x86_64-3.7/xx.cpython-37m-aarch64-linux-android.so /data/local/tmp
[100%] /data/local/tmp/xx.cpython-37m-aarch64-linux-android.so

$ adb shell
shell@ASUS_Z00E_2:/ $ cd /data/local/tmp
shell@ASUS_Z00E_2:/data/local/tmp $ . ./python3/tools/env.sh
shell@ASUS_Z00E_2:/data/local/tmp $ python3.7m
Python 3.7.0a0 (default:3d660ed2a60e+, Nov 23 2016, 20:22:14) 
[GCC 4.2.1 Compatible Android Clang 3.8.256229 ] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import xx
>>> xx
<module 'xx' from '/data/local/tmp/xx.cpython-37m-aarch64-linux-android.so'>
>>>

Here's my xxmodule.c:

#include "Python.h"

PyDoc_STRVAR(module_doc,
"This is a template module just for instruction.");

static struct PyModuleDef xxmodule = {
    PyModuleDef_HEAD_INIT,
    "xx",
    module_doc,
    0,
    NULL,
    NULL,
    NULL,
    NULL,
    NULL
};

PyMODINIT_FUNC
PyInit_xx(void)
{
    return PyModuleDef_Init(&xxmodule);
}

And setup.py:

from distutils.core import setup, Extension

module1 = Extension('xx',
                    sources=['xxmodule.c'])

setup(name='PackageName',
      version='1.0',
      description='This is a demo package',
      ext_modules=[module1])

Both the host and target Python are built from a6e59a2e880e

There's a little bug in the built filename: build/lib.linux-x86_64-3.7/xx.cpython-37m-aarch64-linux-android.so, which should be build/lib.linux-aarch64-3.7/xx.cpython-37m-aarch64-linux-android.so.

Also, I guess there may be quirks if NDK or the cross-built CPython is at different locations than built-time configurations. Those issues can be left to the future.