Ref T13544. These are passthrough flags that control the behavior of the "arc lint" subprocess.
I suspect all use cases of "--apply-patches" are better served by a prompt default via "arc prompts".
I suspect all use cases of "--never-apply-patches" are better served by either using prompt defaults or by using "--nolint", which accomplishes the same goal ("ignore lint") much faster. If you want to look at lint and make a nuanced decision about what to act on, you can use "arc lint".