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> At a guess, the problem is because in atexit_callfuncs():
> 
> module = PyState_FindModule(&atexitmodule);
> if (module == NULL)
> return;
In #31901, I solved this problem by getiing rid of PyState_FindModule in the atexit code, using module state and PEP-489 multiphase initialization.
This needed some changes in the pystate and pylifecycle code, so the specific interpreter has a reference to its own atexit module. This way, Py_EndInterpreter() is able to call the callbacks for the given interpreter.
See: https://github.com/python/cpython/pull/4611