基于@hoefling的回答，我能够打包resource_folder并混淆了二进制a.so文件。

setup.py的配方

from Cython.Distutils import build_ext
from Cython.Build import cythonize
from setuptools.extension import Extension
from setuptools.command.build_py import build_py as build_py_orig
from pathlib import Path
from setuptools import find_packages, setup, Command
import os
import shutil

here = os.path.abspath(os.path.dirname(__file__))    
packages = find_packages(exclude=('tests',))

def get_package_files_in_directory(directory):
    paths = []
    for (path, directories, filenames) in os.walk(directory):
        for filename in filenames:
            paths.append(os.path.join('..', path, filename))
    return paths
#to copy the __init__.py as specified in above references links

class MyBuildExt(build_ext):
    def run(self):
        build_ext.run(self)

        build_dir = Path(self.build_lib)
        root_dir = Path(__file__).parent

        target_dir = build_dir if not self.inplace else root_dir

        self.copy_file(Path('main_folder') / '__init__.py', root_dir, target_dir)


    def copy_file(self, path, source_dir, destination_dir):
        if not (source_dir / path).exists():
            return

        shutil.copyfile(str(source_dir / path), str(destination_dir / path))

#as specified by @hoefling to ignore .py and not resource_folder
class build_py(build_py_orig):
    def build_packages(self):
        pass

setup(
    packages=find_packages(),  # needed for obfuscation
    ext_modules=cythonize(
        [
           Extension("main_folder.*", ["main_folder/*.py"])

        ],
        build_dir="build",
        compiler_directives=dict(
        always_allow_keywords=True
        )),
    package_data={p: get_package_files_in_directory(os.path.join(here, p, 'resource_folder')) for p in packages}, #package_data as found in another reference
    cmdclass={
        'build_py': build_py
    },
    entry_points={
    },
)

创建混淆的* .whl软件包命令集

python setup.py build_ext  #creates the a.so
python setup.py build_py   #copies the resource_folder excluding .py
python setup.py bdist_wheel # then whl generation