Beating on the dead horse a little more... (stock phrase :)
The thing that bugs me about "doesn't mean what you think" phrase (in general... forget its use in this thread) is that in my opinion no one can know what someone else is thinking. It's presumptuous to imply that one knows what someone else is thinking. At least, it comes across that way to me. The issue seems to be that things can have multiple definitions. And two people may be operating with different definitions. But unless someone clearly states x means y, then I find it presumptuous for anyone to say to that someone, "I know what your definition is". What they are really doing is taking a guess. In my opinion.
The examples of stock phrases you gave are qualitatively different from something like "doesn't mean what you think it means". I'm not sure how to describe the difference. Maybe they are metaphors? I don't know. But they are different. For one, they don't on their own presume anything about anyone else.
Repetition is fine up to a point. Maybe it's like a song. Even if it's a good song, if you listen to it too many times in a short period of time, it loses something. You may not even want to hear it anymore. Too much of a good thing. Stock phrase #2.