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Thanks for the report and patience. This behavior is still reproducible on master as of f55c64c632 . I am adding Raymond as part of triaging who might have a better explanation about this. Raymond, feel free to remove yourself if this is not relevant.
A slightly cleaned up version of the program with repl statements removed for reference : 
class O(object):
 pass
class M(type):
 pass
class N(type):
 pass
class A(O, metaclass=M):
 pass
class B(O, metaclass=N):
 pass
print(B.__bases__)
print(B.__mro__)
print(type(B))
print(type(A))
print(issubclass(type(B), type(A)))
class C(A, metaclass=N):
 pass
class D(B, A):
 pass
class E(B, metaclass=N):
 pass