Scouting around the CPython codebase a bit, I speculate that the cause of this behavior is that PyErr_GivenExceptionMatches() in errors.c uses PyType_IsSubtype() [which simply walks a class's __mro__ checking for pointer equality] rather than PyObject_IsSubclass()/PyObject_IsInstance() [which are smart enough to consult __subclasscheck__()/__instancecheck__() if they exist].

Of course, the more important issue here is whether this behavior is intended or not. I surmise python-dev needs to have a discussion about it?