`more than one target found for cross-reference` warning appeared after upgrading to `sphinx==5.2.3` and `sphinx-autoapi>=2.0.0`

Hey! Our build is popping up a new warning after upgrading to the latest sphinx and autoapi.

/home/sam/Code/specs/autoapi_mre/doc/autoapi/file3/index.rst:33:more than one target found for cross-reference 'Transaction': file1.Transaction, file2.Transaction

Here's the setup:

file1.py

class Transaction:
    pass

file2.py

class Transaction:
    pass

file3.py

from typing import Union

Transaction = Union[int, str]


def foo(x: Transaction):
    pass

conf.py

project = "MRE"
copyright = "2021, Foo"
author = "Foo"

extensions = [
    "autoapi.extension",
]

autoapi_type = "python"
autoapi_dirs = ["../mre"]

templates_path = ["_templates"]

highlight_language = "python3"

add_module_names = False

autodoc_typehints = "signature"

exclude_patterns = []

html_theme = "alabaster"
html_static_path = []

Repro

You can find the whole repro here: https://github.com/SamWilsn/autoapi-mre

Build with: tox -e doc.

Start by reproducing the warning with the linked MRE and tox -e doc, then inspect doc/conf.py and the generated doc/autoapi/file3/index.rst alongside the file1.py, file2.py, and file3.py examples. Trace how the Sphinx 5.2.3 and sphinx-autoapi 2.0.0 setup resolves the Transaction cross-reference; done means the reported regression is understood and the warning has a verified resolution or a focused regression test.