Interesting, I didn't ever put the stir bar in the boiling wort because I wasn't sure if it could take the heat. If it can, in it is going to go from now on.
On the cold water bath subject, I don't know about others but I always keep the level of the bath so that the cold water is at a lower level than the wort. I think I heard that you can have high temperature differentials across the borosilicate glass if you have material on the other side of it. So, if I put it in a deep water bath maybe it would crack in the section that is empty (top). That sounded reasonable to me since you can put it on the stove and it doesn't break, and the burner is pretty hot but is only exposed to the area with liquid on the other side of the glass.
Thanks for the input!