I , too, have been confused by the fringe from time to time, especially at St. Andrews. If it looks like the pin is in, you can always check the lie under the golf ball in the lower right corner of your window. Or, you could just pull it yourself and be done with it.
The reason the pin is 'visible' on putts is to mark the hole. There are plenty of examples I can think of why it's necessary. Long distances and the humps on St. Andrews hiding the hole are only a couple.
If you hit a flagstick while putting, you were on the fringe.....and consequently had other options for your shot, too.