I work with old and new code bases used by many clients in complicated setups, but adding a warning to stderr while stdout was left untouched, and proper exit codes maintained, was hardly, if ever, a problem so far.
Of course, there's always some unpleasant exception, but it's rare.
And of course, I also understand that the author might have found themselves not only in one of those rare-ish instances, but also one where reasoning with the other side was fruitless.