This icon seems to be largely a hold-over from the classic MacOS days (before Mac OS X). Apple is now recommending that you only ever use either the application icon or the yellow caution icon (called, interestingly, the
NSCriticalAlertStyle). The latter is, apparently, supposed to be used in the same situations that the previous "stop" icon was used (namely in situations of possible or probable data loss):
This type of badged alert is appropriate only if the user is performing a task that might result in the inadvertent and unexpected destruction of data.
In classic MacOS, alerts never used the application icon; instead they used one of the following icons (these icons taken from The Interface Mafia):
A clue to why the icon was deemphasised (or even removed) in OS X is the fact that the "stop" icon was apparently supposed to be replaced in other localisations:
The stop icon is replaced by another icon in some countries where an open palm has offensize meanings.
Since Carbon applications were the main way for classic Mac apps to be ported to Mac OS X, it's likely that the icon was produced (without the potentially-offensive gesture) to enable apps to run cross-platform.
It seems fairly clear to me that Apple would prefer you didn't use it going forward.