Some of the exceptions among the modules you listed are:

Lib/test/test_warnings.py:420 has a class specific for the C module.

Lib/test/json_tests/test_dump.py:34 has an additional test specific for the C module.
Lib/test/json_tests/test_speedups.py is specific for the C module.

Lib/test/test_functools.py:199 is specific to the Python module.
Lib/test/test_functools.py:207 different tests depending on the version.

Unless these additional methods are defined separately and somehow added to the two classes returned by pep399_tests.create_test_cases(ExampleTest), it would be necessary to create additional classes using the current idiom and then get the modules from pep399_tests.cmodule/pep399_tests.pycmodule, e.g.:

# the two "normal" tests
TestPyDump, TestCDump = pep399_tests.create_test_cases(DumpTest)

# the additional test for the C module
@unittest.skipUnless(pep399_tests.cmodule, 'requires _json')
class TestCDump2(unittest.TestCase)
    module = pep399_tests.cmodule
    @bigmemtest(size=_1G, memuse=1)
    def test_large_list(self, size):
        ...

FWIW I won't change the json tests, because I already wrote them in a way that most of the code is defined in __init__.py and shared in all the other test files.