main.py

import one
import two

print(one.stub_types())
print(two.stub_types())

# Prints
# {'x': <class 'one.Homonymous'>}
# {'x': <class 'two.Homonymous'>}

one.py

import typing

class Homonymous:
    def __repr__(self):
        return 'one.Homonymous'


def stub(x: 'Homonymous'):
    pass


def stub_types():
    return typing.get_type_hints(stub)

two.py

import typing

class Homonymous:
    def __repr__(self):
        return 'two.Homonymous'


def stub(x: 'Homonymous'):
    pass


def stub_types():
    return typing.get_type_hints(stub)