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The objection to the proposed fix is not valid in light
of the bug #1303614, which gives a general way to abuse
subclassing to allow the __dict__ of an instance to be
assigned to and deleted, even when it should not be allowed.  So I wouldn't worry too much about the case I pointed up, because it should be fixed together with #1303614 (though I don't really know how).  For now I would be happy with just checking that subclassing a non-heap type doesn't move the dict within the structure.

The same remark probably applies to the weakref field.  Both cases could be fixed by being more careful in typeobject.c:extra_ivars(): PyModule_Type should be considered to have extra_ivars() when compared to PyBaseObject_Type.  This could be achieved by skipping the "t_size -= ..." part if "type" is not a heap type.  Indeed, for non-heap types we should not try to consider that an extra dict or weakref slot is not important, because the C code probably accesses this extra slot directly, as in the case of moduleobject.c.