Example code for https://stackoverflow.com/questions/60776671/inline-type-annotations-vs-stub-results-in-different-mypy-behaviour

failing.py

class Foo:
    def bar(self, *baz):
        raise NotImplementedError


class SubFoo(Foo):
    def bar(self, baz: float) -> str:
        pass

failing.pyi

from typing import Generic, TypeVar, Callable

T_co = TypeVar("T_co", covariant=True)

class Foo(Generic[T_co]):
    bar: Callable[..., T_co]

succeeding.py

class Foo:
    def bar(self, *baz):
        raise NotImplementedError


class SubFoo(Foo):
    def bar(self, baz):
        pass

succeeding.pyi

from typing import Generic, TypeVar, Callable

T_co = TypeVar("T_co", covariant=True)

class Foo(Generic[T_co]):
    bar: Callable[..., T_co]

class SubFoo(Foo):
    bar: Callable[[float], str]

To reproduce the behavior from the question run

git clone https://gist.github.com/4439755ed0add02dd22eab81c5d7d34e.git tmp
cd tmp
python3.6 -m mypy succeeding.py
python3.6 -m mypy failing.py