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test_threading: test_threads_join_2() was added by commit 7b47699 in 2013, but the test failed randomly since it was added. It's just that failures were ignored until I created https://bugs.python.org/issue36402 last March.
In fact, when the test failed randomly on buildbot (with tests run in parallel), it was fine since test_threading was re-run alone and then the test passed. The buildbot build was seen overall as a success. Previous issues were closed (see my previous comment).
The test shows the bug using subinterpreters (Py_EndInterpreter), but the bug also exists in Py_Finalize() which hash the same race condition (it also calls threading._shutdown()). It's just that Py_EndInterpreter() is stricter, it contains this assertion:
 if (tstate != interp->tstate_head || tstate->next != NULL)
 Py_FatalError("Py_EndInterpreter: not the last thread");
Attached py_finalize.patch adds the same assertion to Py_Finalize.
I added test_threading.test_finalization_shutdown() to PR 13948. If you run test_finalization_shutdown() with py_finalize.patch, Py_Finalize() fails with a similar assertion error.
But py_finalize.patch is incompatible with the principle of daemon threads and so cannot be commited.