as that is the case, how about this as a solution:

def formatannotation(annotation, base_module=None):
    if isinstance(annotation, type):
        if annotation.__module__ in ('builtins', base_module):
            return annotation.__qualname__
        elif annotation.__module__ in ('typing', base_module):       
            return repr(annotation).replace("typing.","")
        return annotation.__module__+'.'+annotation.__qualname__
    return repr(annotation)

the same way that it check for builtins, do it for typing and clean up a little. 

With that change the result with the example is

>>> help(foo)
Help on function foo in module __main__:

foo(data:List[Any]) -> Iterator[Tuple[int, Any]]

>>>