What's more critical or dangerous? A machine suddenly unexpectingly starting or one stopping. In most cases it is more important that machinery doesn't start unexpectedly and it takes a required conscious effort to start it. So, a flush mount is used so that the operator has to push it with his finger and not slap at it or accidentally lean on it. The stop on the otherhand is often extended so that it can be slapped at quickly to stop the machine. It could be argued however, that the kind of quick stop like that should be done with a mushroom head easily accessible and that a controlled stop (again taking a conscious effort) could also be flush too.
Another reason to use an extended head, although I don't like them, is for maintained stop. You can buy an adapter that once you push the extended head in, your flip it over the PB and it holds it in. Again, I'd rather use a maintained push/pull mushroom head for that. Some people use these for maintained jog too (with the flip adapter) and I REALLY think those are unsafe, unless you have readily accessible pull cords everywhere.